[English] 日本語
Yorodumi
- PDB-3may: Crystal structure of a secreted Mycobacterium tuberculosis heme-b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3may
TitleCrystal structure of a secreted Mycobacterium tuberculosis heme-binding protein
ComponentsPOSSIBLE EXPORTED PROTEIN
Keywordsheme-binding protein / helical protein
Function / homology
Function and homology information


heme transport / heme binding / extracellular region
Similarity search - Function
Haemophore, haem-binding domain / Hemophore Rv0203 / Haemophore, haem-binding / Haemophore, haem-binding domain superfamily / Haemophore, haem-binding / F1FO ATP Synthase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MHB domain-containing protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGoulding, C.W. / Chim, N.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Discovery and characterization of a unique mycobacterial heme acquisition system.
Authors: Tullius, M.V. / Harmston, C.A. / Owens, C.P. / Chim, N. / Morse, R.P. / McMath, L.M. / Iniguez, A. / Kimmey, J.M. / Sawaya, M.R. / Whitelegge, J.P. / Horwitz, M.A. / Goulding, C.W.
History
DepositionMar 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POSSIBLE EXPORTED PROTEIN
B: POSSIBLE EXPORTED PROTEIN
C: POSSIBLE EXPORTED PROTEIN
D: POSSIBLE EXPORTED PROTEIN
E: POSSIBLE EXPORTED PROTEIN
G: POSSIBLE EXPORTED PROTEIN
F: POSSIBLE EXPORTED PROTEIN
H: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)83,2788
Polymers83,2788
Non-polymers00
Water1,00956
1
A: POSSIBLE EXPORTED PROTEIN
B: POSSIBLE EXPORTED PROTEIN
C: POSSIBLE EXPORTED PROTEIN
D: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,6394
Polymers41,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-71 kcal/mol
Surface area16900 Å2
MethodPISA
2
E: POSSIBLE EXPORTED PROTEIN
G: POSSIBLE EXPORTED PROTEIN
F: POSSIBLE EXPORTED PROTEIN
H: POSSIBLE EXPORTED PROTEIN


Theoretical massNumber of molelcules
Total (without water)41,6394
Polymers41,6394
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-74 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.671, 72.671, 173.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein
POSSIBLE EXPORTED PROTEIN / Rv0203


Mass: 10409.718 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 36-136
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT0213, Rv0203 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: O53654
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.76 Å3/Da / Density % sol: 55.39 %

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9792, 0.9795, 1.04
DetectorDate: Jun 15, 2002
RadiationMonochromator: Si III channel / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
31.041
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.51
11-H, K, -L20.49
ReflectionResolution: 2.5→100 Å / Num. obs: 31089 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.9 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 31.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→72.68 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.594 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2557 1595 5.2 %RANDOM
Rwork0.1947 ---
obs0.19776 29261 99.49 %-
all-30856 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.279 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→72.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 0 56 5379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215410
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.9727367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.08626.211190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.34515869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6241516
X-RAY DIFFRACTIONr_chiral_restr0.1340.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214004
X-RAY DIFFRACTIONr_mcbond_it1.4451.53701
X-RAY DIFFRACTIONr_mcangle_it2.35725922
X-RAY DIFFRACTIONr_scbond_it3.92731709
X-RAY DIFFRACTIONr_scangle_it5.9874.51445
X-RAY DIFFRACTIONr_rigid_bond_restr2.29635278
LS refinement shellResolution: 2.5→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 138 -
Rwork0.193 2037 -
obs--95.81 %
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)
12.3517-1.2084-1.18411.34590.12183.3512-0.0605-0.2756-0.1956-0.12040.11870.12030.2090.1041-0.05820.2239-0.09040.02720.22650.06040.345111.51710.09913.724
22.6797-0.5741-3.14190.22241.06485.6336-0.2506-0.0993-0.2568-0.03220.10310.0374-0.07130.09860.14750.1894-0.02820.00550.30920.0420.3233-2.90815.0422.574
31.6367-0.35731.22850.9946-0.36265.3294-0.4083-0.05580.28620.02410.2728-0.3699-0.2376-0.04250.13550.1272-0.0312-0.01660.1722-0.04170.3937-10.951-8.85723.213
42.85350.04162.39932.3534-0.747.0565-0.03090.43570.18880.01980.0112-0.2260.14830.51060.01970.05570.05220.03780.2553-0.00590.34181.717-13.69631.004
52.91590.5927-3.34950.3206-0.20444.9997-0.19540.1344-0.2576-0.110.083-0.11890.0056-0.06340.11240.22770.04560.05140.2397-0.0080.332339.19251.37331.396
62.77360.9757-1.61620.7777-0.19254.743-0.18430.2934-0.28970.17560.19-0.06770.2627-0.0354-0.00570.16510.07750.02280.2063-0.03540.339824.79146.4640.267
71.018-1.35241.39472.4687-0.56624.3959-0.1553-0.12040.02910.18140.1154-0.0188-0.1952-0.22660.03990.2039-0.0135-0.00770.242-0.00520.387347.15527.45530.834
83.3794-0.73582.05961.04850.49576.1409-0.0345-0.38470.11270.0311-0.07480.23550.0379-0.550.10930.0852-0.05560.00940.26860.03030.383134.19921.80322.592
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 125
2X-RAY DIFFRACTION2B40 - 132
3X-RAY DIFFRACTION3C38 - 134
4X-RAY DIFFRACTION4D40 - 133
5X-RAY DIFFRACTION5E38 - 131
6X-RAY DIFFRACTION6F40 - 125
7X-RAY DIFFRACTION7G39 - 135
8X-RAY DIFFRACTION8H38 - 133

+
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