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- PDB-2wb1: The complete structure of the archaeal 13-subunit DNA-directed RN... -

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Basic information

Entry
Database: PDB / ID: 2wb1
TitleThe complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase
Components
  • (DNA-DIRECTED RNA POLYMERASE ...) x 12
  • DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
KeywordsTRANSCRIPTION / RNA-POLYMERASE / MULTI-SUBUNIT ENZYME
Function / homology
Function and homology information


RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase ...RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription elongation by RNA polymerase I / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / transcription by RNA polymerase II / protein dimerization activity / nucleotide binding / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G ...Arc Repressor Mutant, subunit A - #1950 / Immunoglobulin-like - #2940 / Dihydrolipoamide Transferase - #40 / Helix Hairpins - #930 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2940 / N-terminal domain of TfIIb - #80 / RNA polymerase Rpo13 subunit HTH domain / RNA polymerase Rpo13 subunit HTH domain / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase, subunit G / DNA polymerase; domain 1 - #390 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo12 / Dihydrolipoamide Transferase / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain / RNA polymerase ii / N-terminal domain of TfIIb / RNA polymerase Rpb7-like, N-terminal domain / Hypothetical Protein Ta0175; Chain: A, domain 2 - #20 / HRDC domain superfamily / DCoH-like / RNA polymerase alpha subunit dimerisation domain / Hypothetical Protein Ta0175; Chain: A, domain 2 / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 / DNA-directed RNA polymerase, subunit 2, domain 6 / Alpha-Beta Plaits - #20 / Barwin-like endoglucanases - #20 / Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase II, Rpb2 subunit, wall domain / Barwin-like endoglucanases / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / Other non-globular / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Rubrerythrin, domain 2 / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Gyrase A; domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / Homeodomain-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / : / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases N / 8 kDa subunit / RNA polymerases N / 8 Kd subunits signature. / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1 / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase subunit Rpo11 / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase, subunit H/Rpb5 C-terminal / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Single Sheet / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / S1 domain / Helix non-globular / Beta Complex / Special / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6
Similarity search - Domain/homology
FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 ...FE3-S4 CLUSTER / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo8 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo13
Similarity search - Component
Biological speciesSULFOLOBUS SHIBATAE (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsKorkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A.
CitationJournal: Plos Biol. / Year: 2009
Title: Evolution of Complex RNA Polymerase: The Complete Archaeal RNA Polymerase Structure
Authors: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A.
History
DepositionFeb 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
B: DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
C: DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
D: DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
E: DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
F: DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
G: DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
H: DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
I: DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
J: DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
K: DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
L: DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
M: DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
N: DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
O: DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
P: DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
Q: DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
R: DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
S: DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
T: DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
U: DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
V: DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
W: DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
X: DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
Y: DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
Z: DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)812,67140
Polymers811,37726
Non-polymers1,29414
Water00
1
A: DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
B: DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
C: DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
D: DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
E: DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
F: DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
G: DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
H: DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
K: DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
L: DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
N: DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
P: DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
Q: DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,33620
Polymers405,68913
Non-polymers6477
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area87970 Å2
ΔGint-557.5 kcal/mol
Surface area230360 Å2
MethodPQS
2
I: DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT
J: DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT
M: DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT
O: DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT
R: DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT
S: DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT
T: DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT
U: DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT
V: DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT
W: DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT
X: DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT
Y: DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT
Z: DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,33620
Polymers405,68913
Non-polymers6477
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area71930 Å2
ΔGint-508.8 kcal/mol
Surface area246870 Å2
MethodPQS
Unit cell
Length a, b, c (Å)196.095, 211.871, 238.905
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11W
21A
12Y
22C
13R
23B
14S
24D
15T
25E
16U
26F
17V
27G
18Z
28H
19I
29K
110M
210L
111O
211N
112X
212P
113J
213Q

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111W4 - 879
2111A4 - 879
1121Y11 - 394
2121C11 - 394
1131R8 - 1122
2131B8 - 1122
1141S2 - 264
2141D2 - 264
1151T1 - 177
2151E1 - 177
1161U3 - 92
2161F3 - 92
1171V5 - 117
2171G5 - 117
1181Z9 - 82
2181H9 - 82
1191I11 - 92
2191K11 - 92
11101M1 - 91
21101L1 - 91
11111O1 - 64
21111N1 - 64
11121X6 - 48
21121P6 - 48
11131J45 - 76
21131Q45 - 76

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13

NCS oper: (Code: given
Matrix: (-0.99988, 0.0035, 0.01476), (-0.00349, -0.99999, 0.00064), (0.01476, 0.00059, 0.99989)
Vector: 97.1297, 73.7005, -0.1261)

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Components

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DNA-DIRECTED RNA POLYMERASE ... , 12 types, 24 molecules AWBRCYETFUGVHZIKJQLMNOPX

#1: Protein DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT


Mass: 99766.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB53*PLUS
#2: Protein DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT


Mass: 127582.016 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB55*PLUS
#3: Protein DNA-DIRECTED RNA POLYMERASE RPO1C SUBUNIT


Mass: 43779.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB54*PLUS
#5: Protein DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT


Mass: 20324.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB57*PLUS
#6: Protein DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT


Mass: 12822.612 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB58*PLUS
#7: Protein DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT


Mass: 15139.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB59*PLUS
#8: Protein DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT


Mass: 9688.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB60*PLUS
#9: Protein DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT


Mass: 10799.589 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB61*PLUS
#10: Protein DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT


Mass: 12170.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB65*PLUS
#11: Protein DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT


Mass: 10211.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB62*PLUS
#12: Protein DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT


Mass: 7617.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63*PLUS
#13: Protein/peptide DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT


Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB64*PLUS

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Protein , 1 types, 2 molecules DS

#4: Protein DNA-DIRECTED RNA POLYMERASERPO3 SUBUNIT


Mass: 30179.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB56*PLUS

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Non-polymers , 3 types, 14 molecules

#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#15: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#16: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 63.3 % / Description: NONE
Crystal growpH: 6.5
Details: 7MG/ML ENZYME, 150 MM KCL, 100MM SRCL2, 100MM CACODYLATE PH 6.5, 12% PEG MME 5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.52→30.2 Å / Num. obs: 114084 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.1
Reflection shellResolution: 3.52→3.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 62.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
GLRFphasing
MOLREPphasing
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EN0

1en0
PDB Unreleased entry


Resolution: 3.52→30.2 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.809 / SU B: 157.017 / SU ML: 1.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.986 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT FOR THIS ENTRY HAS NOT BEEN FINALIZED AND THEREFORE IT MUST BE CONSIDERED AS A WORK IN PROGRESS. SEE PDB ENTRY 2WAQ FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT FOR THIS ENTRY HAS NOT BEEN FINALIZED AND THEREFORE IT MUST BE CONSIDERED AS A WORK IN PROGRESS. SEE PDB ENTRY 2WAQ FOR FULLY REFINED MODEL. THE B FACTOR REFINEMENT HAS BEEN INITIALLY DONE BY DOMAIN IN CNS THEN OVERALL IN REFMAC. FOR MORE DETAILS SEE REFERENCE PAPER AND PDB ENTRY 2WAQ REFINED STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.384 5721 5 %RANDOM
Rwork0.333 ---
obs0.335 108172 92.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.68 Å2
Baniso -1Baniso -2Baniso -3
1-5.9 Å20 Å20 Å2
2---9.76 Å20 Å2
3---3.86 Å2
Refinement stepCycle: LAST / Resolution: 3.52→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms52713 0 26 0 52739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02253685
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.281.98272601
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23156601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44523.7532369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.707159951
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07315436
X-RAY DIFFRACTIONr_chiral_restr0.0850.28285
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0239716
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.226518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.235593
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.21517
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.2112
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight positional / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11W66910.02
12A66910.02
21Y28330.02
22C28330.02
31R86520.03
32B86520.03
41S20710.02
42D20710.02
51T13850.02
52E13850.02
61U7020.01
62F7020.01
71V9020.02
72G9020.02
81Z6100.02
82H6100.02
91I6590.03
92K6590.03
101M7080.02
102L7080.02
111O5140.02
112N5140.02
121X3460.02
122P3460.02
131J2560.02
132Q2560.02
LS refinement shellResolution: 3.52→3.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 300 -
Rwork0.396 4777 -
obs--57.12 %
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)
10.73690.0747-0.11852.1080.03950.7895-0.0265-0.2955-0.08590.28220.08730.02390.00810.0138-0.0608-0.04760.0131-0.055-0.15130.0236-0.23226.651318.773365.6915
20.7246-0.2476-0.03080.9763-0.37321.0889-0.0521-0.28220.00860.2720.0264-0.5512-0.06380.38270.02570.18260.0046-0.13370.0103-0.14680.098431.321521.305180.0991
30.8140.1126-0.05561.9578-0.17710.8095-0.0896-0.2023-0.36440.10150.06030.0239-0.02390.04190.0293-0.0846-0.0408-0.037-0.17510.0491-0.10535.1948-13.022458.3518
40.46590.7510.11941.21090.16742.0348-0.10190.3018-0.0268-0.93860.1830.38030.1311-0.3328-0.08110.2373-0.1601-0.15130.03110.13970.07-6.192613.353213.8534
56.9070.4433-6.84392.0339-1.74019.46640.3276-0.47240.30381.09970.1073-0.0685-0.1217-0.711-0.4350.00010.0001-0.00030-0.00010.0002-38.640349.2722100.4601
68.58351.3629-5.4793.1892.71237.81430.5954-0.59121.25960.1358-0.19690.6003-0.20020.3541-0.39850.0001-0.000200.00010.00030.0001-35.074460.4281105.3319
76.17350.8384-2.05228.4973-2.79352.9113-0.52350.84390.3322-0.19020.5072-0.6781-0.31340.45870.0162-0.0001-0.00010-0.0001-0.0002034.376247.554922.9444
81.2882-0.65692.38536.74422.47046.5373-0.0333-0.66050.37090.94720.1063-0.4743-0.25590.8288-0.073-0.0002-0.00040.000400.0003-0.000125.899939.68290.3013
94.8579-2.16170.6053.3671-0.10110.6965-0.45120.27641.0720.47630.19020.5236-0.21630.54110.261-0.00120.0004-0.0010.0002-0.00060.0001-2.237449.676867.0173
100.5787-1.03970.11495.0563-5.6159.1977-0.0350.23380.09350.12040.05450.3665-0.9461-0.5512-0.0196-0.00050.0014-0.0001-0.0006-0.00080.0001-4.951438.652420.386
110.28810.0221.96420.00170.1513.3893-0.46030.2363-0.5617-0.95470.8992-0.05690.1864-0.0445-0.4389-0.00060.00010.0005-0.0001-0.0007-0.0004-1.9708-5.801220.0136
124.04963.31530.31537.2973-1.24578.3548-0.3766-0.0122-0.5959-1.15850.39860.4981.2881-1.1911-0.0220.0001-0.00020.00030.0004-0.00060.0003-30.1529-14.6440.8412
130.28-0.52423.58932.801-10.73646.5055-0.6143-1.5238-0.4791.00810.9293-0.30990.8405-0.7499-0.31490.0003-0.0004-0.0008-0.0004-0.0001-0.000516.082644.0614106.1974
140.88640.04250.16691.7342-0.11110.91330.054-0.31410.05590.15610.0229-0.0103-0.175-0.0343-0.0769-0.2462-0.1094-0.1105-0.2061-0.0067-0.189291.620654.958865.5998
150.7519-0.2845-0.16431.6477-0.03160.971-0.0467-0.3403-0.07270.46420.0390.5568-0.1612-0.38360.0077-0.5538-0.0312-0.09340.14260.11990.135667.256652.43480.0856
160.72190.18690.09351.8285-0.01940.51320.019-0.23530.2939-0.2105-0.0201-0.0812-0.2762-0.01060.00110.0105-0.0622-0.1307-0.1345-0.0585-0.168892.542886.729258.3104
170.6911.0213-0.09651.5095-0.14361.7854-0.00080.45270.0113-0.84120.0642-0.42450.05040.3155-0.06340.2002-0.1480.10570.0285-0.11770.058102.931360.477213.6807
186.90170.35816.00960.7667-0.00297.85730.5216-0.4768-0.11140.5847-0.2652-0.16640.63750.6257-0.2564-0.0016-0.0014-0.0036-0.0005-0.0011-0.0013137.461924.4979100.192
1910.21891.36035.39414.5098-3.32716.62730.342-0.7231-1.19740.3673-0.1109-0.5370.0598-0.2815-0.23110.0001-0.000100.0001-0.00020.0001133.789913.4487105.1889
204.88132.70884.94856.122.07475.11430.57420.5094-0.2281-0.65430.05490.7983-0.2228-0.5296-0.62910-0.00010.0002-0.00010.00020.000162.833426.065123.1309
211.57152.1644-2.6066.0837-3.99564.3747-0.0269-0.5928-0.04940.75680.08230.63680.4877-0.6788-0.05540.00010.00220.0011-0.00010.0004-0.000672.890734.005490.2893
224.82120.85160.26591.3496-0.01410.0178-0.29720.3939-0.6069-0.66010.2837-0.26261.0281-0.48070.01350.0458-0.2263-0.1222-0.00330.12510.0358100.973124.024166.8721
231.53320.31830.04193.73482.18798.62490.34460.3226-0.4615-1.0596-0.0031-0.530.15150.2123-0.3415-0.00090.0013-0.0005-0.00050.0006-0.0001102.096535.131120.2083
240.86211.4576-1.71582.4645-2.9013.4149-0.04780.33490.48-1.06730.2397-0.0420.52510.351-0.1918-0.00090.0002-0.0004-0.00020.0007098.937379.580519.9469
255.25076.592.56838.81292.7365.7139-0.16850.29650.72930.02850.3143-0.2981-0.26180.6931-0.14570.00020.0002-0.00010.00030.00030.0002128.123788.351240.6651
263.92113.9474-1.744613.6503-6.64623.2473-0.3879-1.0295-0.47940.74940.25160.2469-0.4995-0.13710.13630.000300.00050.00010.00010.000282.310632.8211104.862
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 879
2X-RAY DIFFRACTION2C11 - 394
3X-RAY DIFFRACTION3B8 - 1122
4X-RAY DIFFRACTION4D2 - 264
5X-RAY DIFFRACTION5E1 - 177
6X-RAY DIFFRACTION6F3 - 92
7X-RAY DIFFRACTION7G5 - 117
8X-RAY DIFFRACTION8H9 - 82
9X-RAY DIFFRACTION9K11 - 92
10X-RAY DIFFRACTION10L1 - 91
11X-RAY DIFFRACTION11N1 - 64
12X-RAY DIFFRACTION12P6 - 48
13X-RAY DIFFRACTION13Q45 - 76
14X-RAY DIFFRACTION14W4 - 879
15X-RAY DIFFRACTION15Y11 - 394
16X-RAY DIFFRACTION16R8 - 1122
17X-RAY DIFFRACTION17S2 - 264
18X-RAY DIFFRACTION18T1 - 177
19X-RAY DIFFRACTION19U3 - 92
20X-RAY DIFFRACTION20V5 - 117
21X-RAY DIFFRACTION21Z9 - 82
22X-RAY DIFFRACTION22I11 - 92
23X-RAY DIFFRACTION23M1 - 91
24X-RAY DIFFRACTION24O1 - 64
25X-RAY DIFFRACTION25X6 - 48
26X-RAY DIFFRACTION26J47 - 81

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