[English] 日本語
Yorodumi
- PDB-3oqt: Crystal structure of Rv1498A protein from mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oqt
TitleCrystal structure of Rv1498A protein from mycobacterium tuberculosis
ComponentsRv1498A PROTEIN
KeywordsFLAVOPROTEIN / DODECIN / FLAVIN BINDING
Function / homology
Function and homology information


nucleotide binding / extracellular region
Similarity search - Function
Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dodecin family protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsLiu, F. / Xiong, J. / Kumar, S. / Yang, C. / Li, S. / Ge, S. / Xia, N. / Swaminathan, K.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Structural and biophysical characterization of Mycobacterium tuberculosis dodecin Rv1498A.
Authors: Liu, F. / Xiong, J. / Kumar, S. / Yang, C. / Ge, S. / Li, S. / Xia, N. / Swaminathan, K.
History
DepositionSep 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rv1498A PROTEIN
B: Rv1498A PROTEIN
C: Rv1498A PROTEIN
D: Rv1498A PROTEIN
E: Rv1498A PROTEIN
F: Rv1498A PROTEIN
G: Rv1498A PROTEIN
H: Rv1498A PROTEIN
I: Rv1498A PROTEIN
J: Rv1498A PROTEIN
K: Rv1498A PROTEIN
L: Rv1498A PROTEIN
M: Rv1498A PROTEIN
N: Rv1498A PROTEIN
O: Rv1498A PROTEIN
P: Rv1498A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,60129
Polymers122,20216
Non-polymers39913
Water4,810267
1
A: Rv1498A PROTEIN
B: Rv1498A PROTEIN
C: Rv1498A PROTEIN
D: Rv1498A PROTEIN
hetero molecules

A: Rv1498A PROTEIN
B: Rv1498A PROTEIN
C: Rv1498A PROTEIN
D: Rv1498A PROTEIN
hetero molecules

A: Rv1498A PROTEIN
B: Rv1498A PROTEIN
C: Rv1498A PROTEIN
D: Rv1498A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,93321
Polymers91,65212
Non-polymers2829
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area27320 Å2
ΔGint-90 kcal/mol
Surface area32700 Å2
MethodPISA
2
E: Rv1498A PROTEIN
F: Rv1498A PROTEIN
G: Rv1498A PROTEIN
H: Rv1498A PROTEIN
hetero molecules

E: Rv1498A PROTEIN
F: Rv1498A PROTEIN
G: Rv1498A PROTEIN
H: Rv1498A PROTEIN
hetero molecules

E: Rv1498A PROTEIN
F: Rv1498A PROTEIN
G: Rv1498A PROTEIN
H: Rv1498A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,93321
Polymers91,65212
Non-polymers2829
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
Buried area26980 Å2
ΔGint-73 kcal/mol
Surface area33170 Å2
MethodPISA
3
I: Rv1498A PROTEIN
J: Rv1498A PROTEIN
K: Rv1498A PROTEIN
L: Rv1498A PROTEIN
hetero molecules

I: Rv1498A PROTEIN
J: Rv1498A PROTEIN
K: Rv1498A PROTEIN
L: Rv1498A PROTEIN
hetero molecules

I: Rv1498A PROTEIN
J: Rv1498A PROTEIN
K: Rv1498A PROTEIN
L: Rv1498A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,00224
Polymers91,65212
Non-polymers35112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_454-z-1,x+1/2,-y-1/21
crystal symmetry operation11_444y-1/2,-z-1/2,-x-11
Buried area27650 Å2
ΔGint-83 kcal/mol
Surface area31890 Å2
MethodPISA
4
M: Rv1498A PROTEIN
N: Rv1498A PROTEIN
O: Rv1498A PROTEIN
P: Rv1498A PROTEIN
hetero molecules

M: Rv1498A PROTEIN
N: Rv1498A PROTEIN
O: Rv1498A PROTEIN
P: Rv1498A PROTEIN
hetero molecules

M: Rv1498A PROTEIN
N: Rv1498A PROTEIN
O: Rv1498A PROTEIN
P: Rv1498A PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,93321
Polymers91,65212
Non-polymers2829
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_454-z-1,x+1/2,-y-1/21
crystal symmetry operation11_444y-1/2,-z-1/2,-x-11
Buried area27480 Å2
ΔGint-84 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.946, 143.946, 143.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-106-

CL

21E-107-

CL

31I-114-

NA

41K-105-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 1 - 70 / Label seq-ID: 1 - 70

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL
13MM
14NN
15OO
16PP

-
Components

#1: Protein
Rv1498A PROTEIN


Mass: 7637.628 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT1547, Rv1498.1, Rv1498A / Plasmid: PTO-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8VK10
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 295 K / pH: 5.8
Details: 2M NH4H2PO4SODIUM, 100 MILLIMOLAR TRIS (PH 8.5), temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Apr 20, 2009 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 22825 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 43.9 % / Rsym value: 0.15 / Net I/σ(I): 8.8
Reflection shellResolution: 2.88→2.95 Å / Redundancy: 41.5 % / Rsym value: 0.69 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOLREPphasing
PHASER(CCP4)phasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CC7

2cc7


Resolution: 2.88→20 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.84 / SU B: 18.33 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28285 1163 5.1 %RANDOM
Rwork0.25225 ---
obs0.25382 21544 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.895 Å2
Refinement stepCycle: LAST / Resolution: 2.88→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8576 0 13 267 8856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0218713
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.91911778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.03451104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1923.077416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.929151408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6111580
X-RAY DIFFRACTIONr_chiral_restr0.0870.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026660
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2510.23903
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.25833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2346
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.21027
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.2120
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0530.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5281.55497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7328770
X-RAY DIFFRACTIONr_scbond_it1.10133312
X-RAY DIFFRACTIONr_scangle_it1.9744.53008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 535 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.790.5
2Bmedium positional1.080.5
3Cmedium positional1.190.5
4Dmedium positional1.070.5
5Emedium positional1.010.5
6Fmedium positional0.940.5
7Gmedium positional0.960.5
8Hmedium positional0.980.5
9Imedium positional0.830.5
10Jmedium positional1.260.5
11Kmedium positional2.170.5
12Lmedium positional1.050.5
13Mmedium positional0.960.5
14Nmedium positional0.950.5
15Omedium positional0.980.5
16Pmedium positional0.790.5
1Amedium thermal1.592
2Bmedium thermal1.432
3Cmedium thermal1.62
4Dmedium thermal2.162
5Emedium thermal1.682
6Fmedium thermal0.892
7Gmedium thermal1.112
8Hmedium thermal1.232
9Imedium thermal1.182
10Jmedium thermal1.232
11Kmedium thermal1.342
12Lmedium thermal12
13Mmedium thermal3.152
14Nmedium thermal2.082
15Omedium thermal1.532
16Pmedium thermal1.532
LS refinement shellResolution: 2.878→2.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 98 -
Rwork0.326 1505 -
obs--98.22 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more