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- PDB-4v7g: Crystal Structure of Lumazine Synthase from Bacillus Anthracis -

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Basic information

Entry
Database: PDB / ID: 4v7g
TitleCrystal Structure of Lumazine Synthase from Bacillus Anthracis
Components6,7-dimethyl-8-ribityllumazine synthase
KeywordsTRANSFERASE / RIBOFLAVIN BIOSYNTHESIS
Function / homology
Function and homology information


6,7-dimethyl-8-ribityllumazine synthase / 6,7-dimethyl-8-ribityllumazine synthase activity / riboflavin synthase complex / riboflavin biosynthetic process
Similarity search - Function
Lumazine synthase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Domain/homology
PHOSPHATE ION / 6,7-dimethyl-8-ribityllumazine synthase
Similarity search - Component
Biological speciesBacillus Anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsMorgunova, E. / Illarionov, B. / Saller, S. / Popov, A. / Sambaiah, T. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis.
Authors: Morgunova, E. / Illarionov, B. / Saller, S. / Popov, A. / Sambaiah, T. / Bacher, A. / Cushman, M. / Fischer, M. / Ladenstein, R.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 3JV8, 1VSW, 1VSX
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
AC: 6,7-dimethyl-8-ribityllumazine synthase
AD: 6,7-dimethyl-8-ribityllumazine synthase
AE: 6,7-dimethyl-8-ribityllumazine synthase
AF: 6,7-dimethyl-8-ribityllumazine synthase
AG: 6,7-dimethyl-8-ribityllumazine synthase
AH: 6,7-dimethyl-8-ribityllumazine synthase
AI: 6,7-dimethyl-8-ribityllumazine synthase
AJ: 6,7-dimethyl-8-ribityllumazine synthase
AK: 6,7-dimethyl-8-ribityllumazine synthase
AL: 6,7-dimethyl-8-ribityllumazine synthase
AM: 6,7-dimethyl-8-ribityllumazine synthase
AN: 6,7-dimethyl-8-ribityllumazine synthase
AO: 6,7-dimethyl-8-ribityllumazine synthase
AP: 6,7-dimethyl-8-ribityllumazine synthase
AQ: 6,7-dimethyl-8-ribityllumazine synthase
AR: 6,7-dimethyl-8-ribityllumazine synthase
AS: 6,7-dimethyl-8-ribityllumazine synthase
AT: 6,7-dimethyl-8-ribityllumazine synthase
AU: 6,7-dimethyl-8-ribityllumazine synthase
AV: 6,7-dimethyl-8-ribityllumazine synthase
AW: 6,7-dimethyl-8-ribityllumazine synthase
AX: 6,7-dimethyl-8-ribityllumazine synthase
AY: 6,7-dimethyl-8-ribityllumazine synthase
AZ: 6,7-dimethyl-8-ribityllumazine synthase
A1: 6,7-dimethyl-8-ribityllumazine synthase
A2: 6,7-dimethyl-8-ribityllumazine synthase
A3: 6,7-dimethyl-8-ribityllumazine synthase
A4: 6,7-dimethyl-8-ribityllumazine synthase
BA: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
BC: 6,7-dimethyl-8-ribityllumazine synthase
BD: 6,7-dimethyl-8-ribityllumazine synthase
BE: 6,7-dimethyl-8-ribityllumazine synthase
BF: 6,7-dimethyl-8-ribityllumazine synthase
BG: 6,7-dimethyl-8-ribityllumazine synthase
BH: 6,7-dimethyl-8-ribityllumazine synthase
BI: 6,7-dimethyl-8-ribityllumazine synthase
BJ: 6,7-dimethyl-8-ribityllumazine synthase
BK: 6,7-dimethyl-8-ribityllumazine synthase
BL: 6,7-dimethyl-8-ribityllumazine synthase
BM: 6,7-dimethyl-8-ribityllumazine synthase
BN: 6,7-dimethyl-8-ribityllumazine synthase
BO: 6,7-dimethyl-8-ribityllumazine synthase
BP: 6,7-dimethyl-8-ribityllumazine synthase
BQ: 6,7-dimethyl-8-ribityllumazine synthase
BR: 6,7-dimethyl-8-ribityllumazine synthase
BS: 6,7-dimethyl-8-ribityllumazine synthase
BT: 6,7-dimethyl-8-ribityllumazine synthase
BU: 6,7-dimethyl-8-ribityllumazine synthase
BV: 6,7-dimethyl-8-ribityllumazine synthase
BW: 6,7-dimethyl-8-ribityllumazine synthase
BX: 6,7-dimethyl-8-ribityllumazine synthase
BY: 6,7-dimethyl-8-ribityllumazine synthase
BZ: 6,7-dimethyl-8-ribityllumazine synthase
B1: 6,7-dimethyl-8-ribityllumazine synthase
B2: 6,7-dimethyl-8-ribityllumazine synthase
B3: 6,7-dimethyl-8-ribityllumazine synthase
B4: 6,7-dimethyl-8-ribityllumazine synthase
CA: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
CC: 6,7-dimethyl-8-ribityllumazine synthase
CD: 6,7-dimethyl-8-ribityllumazine synthase
CE: 6,7-dimethyl-8-ribityllumazine synthase
CF: 6,7-dimethyl-8-ribityllumazine synthase
CG: 6,7-dimethyl-8-ribityllumazine synthase
CH: 6,7-dimethyl-8-ribityllumazine synthase
CI: 6,7-dimethyl-8-ribityllumazine synthase
CJ: 6,7-dimethyl-8-ribityllumazine synthase
CK: 6,7-dimethyl-8-ribityllumazine synthase
CL: 6,7-dimethyl-8-ribityllumazine synthase
CM: 6,7-dimethyl-8-ribityllumazine synthase
CN: 6,7-dimethyl-8-ribityllumazine synthase
CO: 6,7-dimethyl-8-ribityllumazine synthase
CP: 6,7-dimethyl-8-ribityllumazine synthase
CQ: 6,7-dimethyl-8-ribityllumazine synthase
CR: 6,7-dimethyl-8-ribityllumazine synthase
CS: 6,7-dimethyl-8-ribityllumazine synthase
CT: 6,7-dimethyl-8-ribityllumazine synthase
CU: 6,7-dimethyl-8-ribityllumazine synthase
CV: 6,7-dimethyl-8-ribityllumazine synthase
CW: 6,7-dimethyl-8-ribityllumazine synthase
CX: 6,7-dimethyl-8-ribityllumazine synthase
CY: 6,7-dimethyl-8-ribityllumazine synthase
CZ: 6,7-dimethyl-8-ribityllumazine synthase
C1: 6,7-dimethyl-8-ribityllumazine synthase
C2: 6,7-dimethyl-8-ribityllumazine synthase
C3: 6,7-dimethyl-8-ribityllumazine synthase
C4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,473,176180
Polymers1,464,62990
Non-polymers8,54790
Water00
1
AA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
AC: 6,7-dimethyl-8-ribityllumazine synthase
AD: 6,7-dimethyl-8-ribityllumazine synthase
AE: 6,7-dimethyl-8-ribityllumazine synthase
AF: 6,7-dimethyl-8-ribityllumazine synthase
AG: 6,7-dimethyl-8-ribityllumazine synthase
AH: 6,7-dimethyl-8-ribityllumazine synthase
AI: 6,7-dimethyl-8-ribityllumazine synthase
AJ: 6,7-dimethyl-8-ribityllumazine synthase
AK: 6,7-dimethyl-8-ribityllumazine synthase
AL: 6,7-dimethyl-8-ribityllumazine synthase
AM: 6,7-dimethyl-8-ribityllumazine synthase
AN: 6,7-dimethyl-8-ribityllumazine synthase
AO: 6,7-dimethyl-8-ribityllumazine synthase
AP: 6,7-dimethyl-8-ribityllumazine synthase
AQ: 6,7-dimethyl-8-ribityllumazine synthase
AR: 6,7-dimethyl-8-ribityllumazine synthase
AS: 6,7-dimethyl-8-ribityllumazine synthase
AT: 6,7-dimethyl-8-ribityllumazine synthase
AU: 6,7-dimethyl-8-ribityllumazine synthase
AV: 6,7-dimethyl-8-ribityllumazine synthase
AW: 6,7-dimethyl-8-ribityllumazine synthase
AX: 6,7-dimethyl-8-ribityllumazine synthase
AY: 6,7-dimethyl-8-ribityllumazine synthase
AZ: 6,7-dimethyl-8-ribityllumazine synthase
A1: 6,7-dimethyl-8-ribityllumazine synthase
A2: 6,7-dimethyl-8-ribityllumazine synthase
A3: 6,7-dimethyl-8-ribityllumazine synthase
A4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules

AA: 6,7-dimethyl-8-ribityllumazine synthase
AB: 6,7-dimethyl-8-ribityllumazine synthase
AC: 6,7-dimethyl-8-ribityllumazine synthase
AD: 6,7-dimethyl-8-ribityllumazine synthase
AE: 6,7-dimethyl-8-ribityllumazine synthase
AF: 6,7-dimethyl-8-ribityllumazine synthase
AG: 6,7-dimethyl-8-ribityllumazine synthase
AH: 6,7-dimethyl-8-ribityllumazine synthase
AI: 6,7-dimethyl-8-ribityllumazine synthase
AJ: 6,7-dimethyl-8-ribityllumazine synthase
AK: 6,7-dimethyl-8-ribityllumazine synthase
AL: 6,7-dimethyl-8-ribityllumazine synthase
AM: 6,7-dimethyl-8-ribityllumazine synthase
AN: 6,7-dimethyl-8-ribityllumazine synthase
AO: 6,7-dimethyl-8-ribityllumazine synthase
AP: 6,7-dimethyl-8-ribityllumazine synthase
AQ: 6,7-dimethyl-8-ribityllumazine synthase
AR: 6,7-dimethyl-8-ribityllumazine synthase
AS: 6,7-dimethyl-8-ribityllumazine synthase
AT: 6,7-dimethyl-8-ribityllumazine synthase
AU: 6,7-dimethyl-8-ribityllumazine synthase
AV: 6,7-dimethyl-8-ribityllumazine synthase
AW: 6,7-dimethyl-8-ribityllumazine synthase
AX: 6,7-dimethyl-8-ribityllumazine synthase
AY: 6,7-dimethyl-8-ribityllumazine synthase
AZ: 6,7-dimethyl-8-ribityllumazine synthase
A1: 6,7-dimethyl-8-ribityllumazine synthase
A2: 6,7-dimethyl-8-ribityllumazine synthase
A3: 6,7-dimethyl-8-ribityllumazine synthase
A4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,118120
Polymers976,41960
Non-polymers5,69860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area255850 Å2
ΔGint-1628 kcal/mol
Surface area252630 Å2
MethodPISA
2
BA: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
BC: 6,7-dimethyl-8-ribityllumazine synthase
BD: 6,7-dimethyl-8-ribityllumazine synthase
BE: 6,7-dimethyl-8-ribityllumazine synthase
BF: 6,7-dimethyl-8-ribityllumazine synthase
BG: 6,7-dimethyl-8-ribityllumazine synthase
BH: 6,7-dimethyl-8-ribityllumazine synthase
BI: 6,7-dimethyl-8-ribityllumazine synthase
BJ: 6,7-dimethyl-8-ribityllumazine synthase
BK: 6,7-dimethyl-8-ribityllumazine synthase
BL: 6,7-dimethyl-8-ribityllumazine synthase
BM: 6,7-dimethyl-8-ribityllumazine synthase
BN: 6,7-dimethyl-8-ribityllumazine synthase
BO: 6,7-dimethyl-8-ribityllumazine synthase
BP: 6,7-dimethyl-8-ribityllumazine synthase
BQ: 6,7-dimethyl-8-ribityllumazine synthase
BR: 6,7-dimethyl-8-ribityllumazine synthase
BS: 6,7-dimethyl-8-ribityllumazine synthase
BT: 6,7-dimethyl-8-ribityllumazine synthase
BU: 6,7-dimethyl-8-ribityllumazine synthase
BV: 6,7-dimethyl-8-ribityllumazine synthase
BW: 6,7-dimethyl-8-ribityllumazine synthase
BX: 6,7-dimethyl-8-ribityllumazine synthase
BY: 6,7-dimethyl-8-ribityllumazine synthase
BZ: 6,7-dimethyl-8-ribityllumazine synthase
B1: 6,7-dimethyl-8-ribityllumazine synthase
B2: 6,7-dimethyl-8-ribityllumazine synthase
B3: 6,7-dimethyl-8-ribityllumazine synthase
B4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules

BA: 6,7-dimethyl-8-ribityllumazine synthase
BB: 6,7-dimethyl-8-ribityllumazine synthase
BC: 6,7-dimethyl-8-ribityllumazine synthase
BD: 6,7-dimethyl-8-ribityllumazine synthase
BE: 6,7-dimethyl-8-ribityllumazine synthase
BF: 6,7-dimethyl-8-ribityllumazine synthase
BG: 6,7-dimethyl-8-ribityllumazine synthase
BH: 6,7-dimethyl-8-ribityllumazine synthase
BI: 6,7-dimethyl-8-ribityllumazine synthase
BJ: 6,7-dimethyl-8-ribityllumazine synthase
BK: 6,7-dimethyl-8-ribityllumazine synthase
BL: 6,7-dimethyl-8-ribityllumazine synthase
BM: 6,7-dimethyl-8-ribityllumazine synthase
BN: 6,7-dimethyl-8-ribityllumazine synthase
BO: 6,7-dimethyl-8-ribityllumazine synthase
BP: 6,7-dimethyl-8-ribityllumazine synthase
BQ: 6,7-dimethyl-8-ribityllumazine synthase
BR: 6,7-dimethyl-8-ribityllumazine synthase
BS: 6,7-dimethyl-8-ribityllumazine synthase
BT: 6,7-dimethyl-8-ribityllumazine synthase
BU: 6,7-dimethyl-8-ribityllumazine synthase
BV: 6,7-dimethyl-8-ribityllumazine synthase
BW: 6,7-dimethyl-8-ribityllumazine synthase
BX: 6,7-dimethyl-8-ribityllumazine synthase
BY: 6,7-dimethyl-8-ribityllumazine synthase
BZ: 6,7-dimethyl-8-ribityllumazine synthase
B1: 6,7-dimethyl-8-ribityllumazine synthase
B2: 6,7-dimethyl-8-ribityllumazine synthase
B3: 6,7-dimethyl-8-ribityllumazine synthase
B4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,118120
Polymers976,41960
Non-polymers5,69860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area259690 Å2
ΔGint-1595 kcal/mol
Surface area251870 Å2
MethodPISA
3
CA: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
CC: 6,7-dimethyl-8-ribityllumazine synthase
CD: 6,7-dimethyl-8-ribityllumazine synthase
CE: 6,7-dimethyl-8-ribityllumazine synthase
CF: 6,7-dimethyl-8-ribityllumazine synthase
CG: 6,7-dimethyl-8-ribityllumazine synthase
CH: 6,7-dimethyl-8-ribityllumazine synthase
CI: 6,7-dimethyl-8-ribityllumazine synthase
CJ: 6,7-dimethyl-8-ribityllumazine synthase
CK: 6,7-dimethyl-8-ribityllumazine synthase
CL: 6,7-dimethyl-8-ribityllumazine synthase
CM: 6,7-dimethyl-8-ribityllumazine synthase
CN: 6,7-dimethyl-8-ribityllumazine synthase
CO: 6,7-dimethyl-8-ribityllumazine synthase
CP: 6,7-dimethyl-8-ribityllumazine synthase
CQ: 6,7-dimethyl-8-ribityllumazine synthase
CR: 6,7-dimethyl-8-ribityllumazine synthase
CS: 6,7-dimethyl-8-ribityllumazine synthase
CT: 6,7-dimethyl-8-ribityllumazine synthase
CU: 6,7-dimethyl-8-ribityllumazine synthase
CV: 6,7-dimethyl-8-ribityllumazine synthase
CW: 6,7-dimethyl-8-ribityllumazine synthase
CX: 6,7-dimethyl-8-ribityllumazine synthase
CY: 6,7-dimethyl-8-ribityllumazine synthase
CZ: 6,7-dimethyl-8-ribityllumazine synthase
C1: 6,7-dimethyl-8-ribityllumazine synthase
C2: 6,7-dimethyl-8-ribityllumazine synthase
C3: 6,7-dimethyl-8-ribityllumazine synthase
C4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules

CA: 6,7-dimethyl-8-ribityllumazine synthase
CB: 6,7-dimethyl-8-ribityllumazine synthase
CC: 6,7-dimethyl-8-ribityllumazine synthase
CD: 6,7-dimethyl-8-ribityllumazine synthase
CE: 6,7-dimethyl-8-ribityllumazine synthase
CF: 6,7-dimethyl-8-ribityllumazine synthase
CG: 6,7-dimethyl-8-ribityllumazine synthase
CH: 6,7-dimethyl-8-ribityllumazine synthase
CI: 6,7-dimethyl-8-ribityllumazine synthase
CJ: 6,7-dimethyl-8-ribityllumazine synthase
CK: 6,7-dimethyl-8-ribityllumazine synthase
CL: 6,7-dimethyl-8-ribityllumazine synthase
CM: 6,7-dimethyl-8-ribityllumazine synthase
CN: 6,7-dimethyl-8-ribityllumazine synthase
CO: 6,7-dimethyl-8-ribityllumazine synthase
CP: 6,7-dimethyl-8-ribityllumazine synthase
CQ: 6,7-dimethyl-8-ribityllumazine synthase
CR: 6,7-dimethyl-8-ribityllumazine synthase
CS: 6,7-dimethyl-8-ribityllumazine synthase
CT: 6,7-dimethyl-8-ribityllumazine synthase
CU: 6,7-dimethyl-8-ribityllumazine synthase
CV: 6,7-dimethyl-8-ribityllumazine synthase
CW: 6,7-dimethyl-8-ribityllumazine synthase
CX: 6,7-dimethyl-8-ribityllumazine synthase
CY: 6,7-dimethyl-8-ribityllumazine synthase
CZ: 6,7-dimethyl-8-ribityllumazine synthase
C1: 6,7-dimethyl-8-ribityllumazine synthase
C2: 6,7-dimethyl-8-ribityllumazine synthase
C3: 6,7-dimethyl-8-ribityllumazine synthase
C4: 6,7-dimethyl-8-ribityllumazine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,118120
Polymers976,41960
Non-polymers5,69860
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area259130 Å2
ΔGint-1587 kcal/mol
Surface area252610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.201, 222.237, 473.488
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: TRP / End label comp-ID: TRP / Auth seq-ID: 2 - 152 / Label seq-ID: 2 - 152

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain AA or chain AB or chain AC or chain AD or chain AEAAA
12chain AA or chain AB or chain AC or chain AD or chain AEABB
13chain AA or chain AB or chain AC or chain AD or chain AEACC
14chain AA or chain AB or chain AC or chain AD or chain AEADD
15chain AA or chain aB or chain aC or chain aD or chain AEAEE
21chain AF or chain AG or chain AH or chain AI or chain AJAFF
22chain AF or chain AG or chain AH or chain AI or chain AJAGG
23chain AF or chain AG or chain AH or chain AI or chain AJAHH
24chain AF or chain AG or chain AH or chain AI or chain AJAII
25chain AF or chain AG or chain AH or chain AI or chain AJAJJ
31chain AK or chain AL or chain AM or chain AN or chain AOAKK
32chain AK or chain AL or chain AM or chain AN or chain AOALL
33chain AK or chain AL or chain AM or chain AN or chain AOAMM
34chain AK or chain AL or chain AM or chain AN or chain AOANN
35chain AK or chain AL or chain AM or chain AN or chain AOAOO
41chain AP or chain AQ or chain AR or chain AS or chain ATAPP
42chain AP or chain AQ or chain AR or chain AS or chain ATAQQ
43chain AP or chain AQ or chain AR or chain AS or chain ATARR
44chain AP or chain AQ or chain AR or chain AS or chain ATASS
45chain AP or chain AQ or chain AR or chain AS or chain ATATT
51chain AU or chain AV or chain AW or chain AX or chain AYAUU
52chain AU or chain AV or chain AW or chain AX or chain AYAVV
53chain AU or chain AV or chain AW or chain AX or chain AYAWW
54chain AU or chain AV or chain AW or chain AX or chain AYAXX
55chain AU or chain AV or chain AW or chain AX or chain AYAYY
61chain AZ or chain A1 or chain A2 or chain A3 or chain A4AZZ
62chain AZ or chain A1 or chain A2 or chain A3 or chain A4A1AA
63chain AZ or chain A1 or chain A2 or chain A3 or chain A4A2BA
64chain AZ or chain A1 or chain A2 or chain A3 or chain A4A3CA
65chain AZ or chain A1 or chain A2 or chain A3 or chain A4A4DA
71chain BA or chain BB or chain BC or chain BD or chain BEBAEA
72chain BA or chain BB or chain BC or chain BD or chain BEBBFA
73chain BA or chain BB or chain BC or chain BD or chain BEBCGA
74chain BA or chain BB or chain BC or chain BD or chain BEBDHA
75chain BA or chain aB or chain aC or chain aD or chain BEBEIA
81chain BF or chain BG or chain BH or chain BI or chain BJBFJA
82chain BF or chain BG or chain BH or chain BI or chain BJBGKA
83chain BF or chain BG or chain BH or chain BI or chain BJBHLA
84chain BF or chain BG or chain BH or chain BI or chain BJBIMA
85chain BF or chain BG or chain BH or chain BI or chain BJBJNA
91chain BK or chain BL or chain BM or chain BN or chain BOBKOA
92chain BK or chain BL or chain BM or chain BN or chain BOBLPA
93chain BK or chain BL or chain BM or chain BN or chain BOBMQA
94chain BK or chain BL or chain BM or chain BN or chain BOBNRA
95chain BK or chain BL or chain BM or chain BN or chain BOBOSA
101chain BP or chain BQ or chain BR or chain BS or chain BTBPTA
102chain BP or chain BQ or chain BR or chain BS or chain BTBQUA
103chain BP or chain BQ or chain BR or chain BS or chain BTBRVA
104chain BP or chain BQ or chain BR or chain BS or chain BTBSWA
105chain BP or chain BQ or chain BR or chain BS or chain BTBTXA
111chain BU or chain BV or chain BW or chain BX or chain BYBUYA
112chain BU or chain BV or chain BW or chain BX or chain BYBVZA
113chain BU or chain BV or chain BW or chain BX or chain BYBWAB
114chain BU or chain BV or chain BW or chain BX or chain BYBXBB
115chain BU or chain BV or chain BW or chain BX or chain BYBYCB
121chain BZ or chain B1 or chain B2 or chain B3 or chain B4BZDB
122chain BZ or chain B1 or chain B2 or chain B3 or chain B4B1EB
123chain BZ or chain B1 or chain B2 or chain B3 or chain B4B2FB
124chain BZ or chain B1 or chain B2 or chain B3 or chain B4B3GB
125chain BZ or chain B1 or chain B2 or chain B3 or chain B4B4HB
131chain CA or chain CB or chain CC or chain CD or chain CECAIB
132chain CA or chain CB or chain CC or chain CD or chain CECBJB
133chain CA or chain CB or chain CC or chain CD or chain CECCKB
134chain CA or chain CB or chain CC or chain CD or chain CECDLB
135chain CA or chain aB or chain aC or chain aD or chain CECEMB
141chain CF or chain CG or chain CH or chain CI or chain CJCFNB
142chain CF or chain CG or chain CH or chain CI or chain CJCGOB
143chain CF or chain CG or chain CH or chain CI or chain CJCHPB
144chain CF or chain CG or chain CH or chain CI or chain CJCIQB
145chain CF or chain CG or chain CH or chain CI or chain CJCJRB
151chain CK or chain CL or chain CM or chain CN or chain COCKSB
152chain CK or chain CL or chain CM or chain CN or chain COCLTB
153chain CK or chain CL or chain CM or chain CN or chain COCMUB
154chain CK or chain CL or chain CM or chain CN or chain COCNVB
155chain CK or chain CL or chain CM or chain CN or chain COCOWB
161chain CP or chain CQ or chain CR or chain CS or chain CTCPXB
162chain CP or chain CQ or chain CR or chain CS or chain CTCQYB
163chain CP or chain CQ or chain CR or chain CS or chain CTCRZB
164chain CP or chain CQ or chain CR or chain CS or chain CTCSAC
165chain CP or chain CQ or chain CR or chain CS or chain CTCTBC
171chain CU or chain CV or chain CW or chain CX or chain CYCUCC
172chain CU or chain CV or chain CW or chain CX or chain CYCVDC
173chain CU or chain CV or chain CW or chain CX or chain CYCWEC
174chain CU or chain CV or chain CW or chain CX or chain CYCXFC
175chain CU or chain CV or chain CW or chain CX or chain CYCYGC
181chain CZ or chain C1 or chain C2 or chain C3 or chain C4CZHC
182chain CZ or chain C1 or chain C2 or chain C3 or chain C4C1IC
183chain CZ or chain C1 or chain C2 or chain C3 or chain C4C2JC
184chain CZ or chain C1 or chain C2 or chain C3 or chain C4C3KC
185chain CZ or chain C1 or chain C2 or chain C3 or chain C4C4LC

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Components

#1: Protein ...
6,7-dimethyl-8-ribityllumazine synthase / Riboflavin synthase beta chain / lumazine synthase


Mass: 16273.656 Da / Num. of mol.: 90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus Anthracis (anthrax bacterium) / Gene: ribH / Plasmid: pNCO-BARibH / Production host: Escherichia coli (E. coli) / Strain (production host): m15
References: UniProt: Q81MB5, 6,7-dimethyl-8-ribityllumazine synthase
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 90 / Source method: obtained synthetically / Formula: PO4

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 36% polypropilenglycol P400, 100mM Tris, 20mM DTT, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2008 / Details: bent cylindrical mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 194243 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.29 / Net I/σ(I): 5.2
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / Num. unique all: 150011 / % possible all: 93.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
FFFEARmodel building
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
FFFEARphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1rvv

1rvv


Resolution: 3.5→14.998 Å / SU ML: 0.63 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 7190 2.01 %RANDOM
Rwork0.235 ---
obs0.236 196243 89.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.004 Å2 / ksol: 0.227 e/Å3
Refinement stepCycle: LAST / Resolution: 3.5→14.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33924 0 150 0 34074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003103908
X-RAY DIFFRACTIONf_angle_d0.599140940
X-RAY DIFFRACTIONf_dihedral_angle_d12.78335658
X-RAY DIFFRACTIONf_chiral_restr0.0416650
X-RAY DIFFRACTIONf_plane_restr0.00117694
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11AA5654X-RAY DIFFRACTIONPOSITIONAL0.019
12AB5654X-RAY DIFFRACTIONPOSITIONAL0.019
13AC5654X-RAY DIFFRACTIONPOSITIONAL0.017
14AD5654X-RAY DIFFRACTIONPOSITIONAL0.016
15AE5654X-RAY DIFFRACTIONPOSITIONAL0.017
16AF5654X-RAY DIFFRACTIONPOSITIONAL0.016
17AG5654X-RAY DIFFRACTIONPOSITIONAL0.015
18AH5654X-RAY DIFFRACTIONPOSITIONAL0.015
19AI5654X-RAY DIFFRACTIONPOSITIONAL0.015
110AJ5654X-RAY DIFFRACTIONPOSITIONAL0.015
111AK5654X-RAY DIFFRACTIONPOSITIONAL0.015
112AL5654X-RAY DIFFRACTIONPOSITIONAL0.015
113AM5654X-RAY DIFFRACTIONPOSITIONAL0.015
114AN5654X-RAY DIFFRACTIONPOSITIONAL0.014
115AO5654X-RAY DIFFRACTIONPOSITIONAL0.015
116AP5654X-RAY DIFFRACTIONPOSITIONAL0.014
117AQ5654X-RAY DIFFRACTIONPOSITIONAL0.015
118AR5654X-RAY DIFFRACTIONPOSITIONAL0.015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.53930.36722610.345111181X-RAY DIFFRACTION86
3.5393-3.58040.36492660.31211676X-RAY DIFFRACTION90
3.5804-3.62340.34192580.323111692X-RAY DIFFRACTION90
3.6234-3.66860.38792240.320211757X-RAY DIFFRACTION90
3.6686-3.71620.35552500.301911742X-RAY DIFFRACTION90
3.7162-3.76630.33872540.289611700X-RAY DIFFRACTION90
3.7663-3.81920.32052490.289311727X-RAY DIFFRACTION90
3.8192-3.87530.30532650.267311647X-RAY DIFFRACTION90
3.8753-3.93480.30912260.256511777X-RAY DIFFRACTION90
3.9348-3.99810.3072760.260511668X-RAY DIFFRACTION90
3.9981-4.06570.33332150.243411739X-RAY DIFFRACTION90
4.0657-4.13810.28662340.239411729X-RAY DIFFRACTION90
4.1381-4.21590.26452160.226111736X-RAY DIFFRACTION90
4.2159-4.30.24532880.21611736X-RAY DIFFRACTION90
4.3-4.39120.28052260.220511735X-RAY DIFFRACTION90
4.3912-4.49070.26432100.208211735X-RAY DIFFRACTION90
4.4907-4.59980.33522120.209511774X-RAY DIFFRACTION90
4.5998-4.72040.31542460.220311718X-RAY DIFFRACTION90
4.7204-4.85480.25822460.20711724X-RAY DIFFRACTION90
4.8548-5.00580.2612250.199311696X-RAY DIFFRACTION90
5.0058-5.17760.19732180.18611784X-RAY DIFFRACTION90
5.1776-5.37580.23962300.185811722X-RAY DIFFRACTION90
5.3758-5.60820.28522190.202911713X-RAY DIFFRACTION90
5.6082-5.88680.28442480.21111734X-RAY DIFFRACTION90
5.8868-6.23070.26972250.217911790X-RAY DIFFRACTION90
6.2307-6.67220.29262470.213211726X-RAY DIFFRACTION90
6.6722-7.27320.2542180.19911802X-RAY DIFFRACTION90
7.2732-8.17330.22132310.174311736X-RAY DIFFRACTION90
8.1733-9.79540.16522400.131311504X-RAY DIFFRACTION88
9.7954-14.99820.21972670.196811830X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13930.02630.16750.27980.30110.3140.0080.0195-0.34610.4721-0.65240.2235-0.08190.18480.14390.0826-0.0512-0.0580.1465-0.25420.517164.948264.48748.2848
20.8737-0.07290.04850.45360.04240.37250.0808-0.02240.0821-0.1036-0.27570.05250.04440.1396-0.03810.1179-0.07280.00590.04060.06540.198523.678495.85338.2997
30.74250.14610.0630.3561-0.03540.16250.0946-0.09820.00470.62090.06940.0972-0.09120.0262-0.07460.19530.0544-0.02040.52480.02810.120849.6982119.5232-10.1665
40.6231-0.18420.01030.1284-0.27530.2743-0.01970.10330.0201-0.4321-0.63820.02570.08240.0656-0.08880.2101-0.0527-0.01560.37480.38360.567265.116564.350168.3863
50.7017-0.085-0.00470.26470.1182-0.0463-0.005-0.0167-0.0023-0.8360.0347-0.02530.22840.07980.00010.3289-0.0258-0.03760.83460.04160.1163107.4749102.650187.0701
60.9377-0.1288-0.06230.4333-0.01450.24910.0703-0.0524-0.0616-0.0781-0.49720.009-0.09440.0569-0.01940.1821-0.0487-0.06060.03650.03420.3406116.854368.633338.5134
71.1970.24190.43510.6676-0.01930.4522-0.08180.07010.1730.33690.6524-0.31830.2774-0.27710.43930.7976-0.6324-0.27820.78090.20180.708643.619436.8205119.3851
80.7113-0.03750.07390.16430.23450.3005-0.23990.01680.0357-0.72880.42760.02670.4318-0.21820.01811.3404-0.1585-0.20260.8046-0.29080.33529.321728.4888167.6971
90.6261-0.3456-0.14370.09250.10670.4107-0.0321-0.0282-0.0229-0.31980.0056-0.17470.27390.31280.43860.7757-0.0826-0.24460.94360.07120.22146.3558-15.1071149.2053
100.9644-0.10150.15640.1968-0.31860.0461-0.28030.19370.10710.01050.8398-0.13690.34-0.6366-0.14831.3043-0.1189-0.20250.39470.14720.8837-13.673255.6024119.1487
110.6609-0.46390.01010.1117-0.16230.6136-0.0536-0.34920.05291.25320.3475-0.3517-0.258-0.32750.22590.6014-0.4355-0.09441.48550.62570.34459.265528.667270.7987
120.8498-0.33480.09710.5852-0.21080.52190.0914-0.17940.09080.68730.08270.1041-0.1273-0.0334-0.44240.4002-0.1743-0.03131.36470.02960.201-46.338415.242289.1659
130.91930.55830.2510.33870.24960.2891.0673-0.8650.0612-0.84740.7530.9730.85230.0345-0.20951.5102-1.07841.15461.4824-0.79271.34521.7624105.4066196.8411
141.15730.59680.28130.5722-0.24120.12820.3263-0.349-0.0316-0.25331.53581.07080.0788-0.262-0.20690.9383-0.06090.64450.5327-0.40071.869948.8288149.6842166.6683
150.95970.56260.32831.24360.3991-0.20680.1518-0.139-0.05440.31370.02730.2293-0.27080.4029-0.12970.8561-0.244-0.12730.6203-0.02820.156754.624893.0135148.2475
160.1637-0.4224-0.3222-0.20950.51170.50651.1189-1.246-0.0976-1.65040.82341.06521.6945-0.18850.13213.656-2.34812.2582.8977-2.03882.17248.8391149.954226.7856
170.91051.14690.11521.42420.18620.13180.9409-0.8617-0.2288-0.85380.69270.30161.3175-0.47010.28392.2363-1.29250.59321.1152-0.53480.559698.8283164.5784196.6641
18-0.2623-0.31270.13420.0055-0.01480.70191.7818-1.75990.0644-1.71140.15050.02652.45930.0874-0.05875.2346-3.8239-0.6124.06880.11370.3441101.9846129.8673245.4025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain AA or chain AB or chain AC or chain AD or chain AE)
2X-RAY DIFFRACTION2(chain AF or chain AG or chain AH or chain AI or chain AJ)
3X-RAY DIFFRACTION3(chain AK or chain AL or chain AM or chain AN or chain AO)
4X-RAY DIFFRACTION4(chain AP or chain AQ or chain AR or chain AS or chain AT)
5X-RAY DIFFRACTION5(chain AU or chain AV or chain AW or chain AX or chain AY)
6X-RAY DIFFRACTION6(chain AZ or chain A1 or chain A2 or chain A3 or chain A4)
7X-RAY DIFFRACTION7(chain BA or chain BB or chain BC or chain BD or chain BE)
8X-RAY DIFFRACTION8(chain BF or chain BG or chain BH or chain BI or chain BJ)
9X-RAY DIFFRACTION9(chain BK or chain BL or chain BM or chain BN or chain BO)
10X-RAY DIFFRACTION10(chain BP or chain BQ or chain BR or chain BS or chain BT)
11X-RAY DIFFRACTION11(chain BU or chain BV or chain BW or chain BX or chain BY)
12X-RAY DIFFRACTION12(chain BZ or chain B1 or chain B2 or chain B3 or chain B4)
13X-RAY DIFFRACTION13(chain CA or chain CB or chain CC or chain CD or chain CE)
14X-RAY DIFFRACTION14(chain CF or chain CG or chain CH or chain CI or chain CJ)
15X-RAY DIFFRACTION15(chain CK or chain CL or chain CM or chain CN or chain CO)
16X-RAY DIFFRACTION16(chain CP or chain CQ or chain CR or chain CS or chain CT)
17X-RAY DIFFRACTION17(chain CU or chain CV or chain CW or chain CX or chain CY)
18X-RAY DIFFRACTION18(chain CZ or chain C1 or chain C2 or chain C3 or chain C4)

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