[English] 日本語
Yorodumi
- PDB-4jes: 1.6A resolution Apo structure of the hemophore HasA from Yersinia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jes
Title1.6A resolution Apo structure of the hemophore HasA from Yersinia pestis (Hexagonal Form)
ComponentsHemophore HasA
KeywordsHEME BINDING PROTEIN / TRANSPORT PROTEIN
Function / homology
Function and homology information


Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Hemophore HasA / Hemophore HasA
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKumar, R. / Lovell, S. / Battaile, K.P. / Rivera, M.
CitationJournal: Biochemistry / Year: 2013
Title: The Hemophore HasA from Yersinia pestis (HasAyp) Coordinates Hemin with a Single Residue, Tyr75, and with Minimal Conformational Change.
Authors: Kumar, R. / Lovell, S. / Matsumura, H. / Battaile, K.P. / Moenne-Loccoz, P. / Rivera, M.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: Hemophore HasA
B: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2879
Polymers42,0502
Non-polymers1,2377
Water4,666259
1
A: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4093
Polymers21,0251
Non-polymers3842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8786
Polymers21,0251
Non-polymers8535
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.071, 75.071, 129.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11B-205-

TAM

21B-205-

TAM

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Hemophore HasA / Secreted hemophore


Mass: 21025.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: hasA, y0314, YP_3127, YPO3922 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q7CL15, UniProt: Q0WA92*PLUS

-
Non-polymers , 5 types, 266 molecules

#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer detailsATOMS N AND C OF THE TAM LIGAND RESIDE ON A SPECIAL POSITION (CRYSTALLOGRAPHIC 3-FOLD). THE ...ATOMS N AND C OF THE TAM LIGAND RESIDE ON A SPECIAL POSITION (CRYSTALLOGRAPHIC 3-FOLD). THE COMPLETE TAM MOLECULE IS GENERATED BY APPLYING THE FOLLOWING SYMMETRY OPERATORS: -Y, X-Y, Z + (0-10) AND -X+Y, -X, Z + (-1 -1 0).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.1 M sodium malonate, 0.1 HEPES, 0.5% (v/v) Jeffamine ED-2001, pH 7.0, vapor diffusion, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→65.013 Å / Num. all: 54313 / Num. obs: 54313 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.01257 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2687 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
SCALA0.1.27data scaling
PHASERphasing
PHENIXdev_1148refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4JER

4jer


Resolution: 1.6→37.535 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.16 / σ(F): 1.72 / Phase error: 18.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2761 5.09 %RANDOM
Rwork0.1611 ---
obs0.1626 54268 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.06 Å2 / Biso mean: 25.8953 Å2 / Biso min: 11.53 Å2
Refinement stepCycle: LAST / Resolution: 1.6→37.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 0 77 259 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092897
X-RAY DIFFRACTIONf_angle_d1.0463895
X-RAY DIFFRACTIONf_chiral_restr0.083405
X-RAY DIFFRACTIONf_plane_restr0.008514
X-RAY DIFFRACTIONf_dihedral_angle_d14.9261092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.62760.25521410.238625542695
1.6276-1.65720.27721280.227125832711
1.6572-1.68910.24431500.229525212671
1.6891-1.72350.23671190.216826112730
1.7235-1.7610.2371490.200225502699
1.761-1.8020.21761610.200125532714
1.802-1.84710.21400.177125672707
1.8471-1.8970.21091440.16425492693
1.897-1.95280.18931410.163825712712
1.9528-2.01580.21431420.160825692711
2.0158-2.08790.1791340.153425932727
2.0879-2.17150.17881320.148425612693
2.1715-2.27030.17141450.14225882733
2.2703-2.390.1531400.145325632703
2.39-2.53970.17891230.152925932716
2.5397-2.73570.18741430.158725672710
2.7357-3.01090.19231440.171325902734
3.0109-3.44630.19741300.164925792709
3.4463-4.3410.1551240.140926112735
4.341-37.54580.20541310.158126342765
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)
12.09260.75491.20641.45060.19662.2461-0.03130.3221-0.1137-0.20190.0305-0.05460.130.091-0.02060.17320.00490.02390.1752-0.01760.175663.5456-18.0081-5.6587
22.2122-0.50590.72332.0612-0.05721.6372-0.02960.0894-0.0944-0.0614-0.00230.30770.0344-0.17020.01940.1258-0.0313-0.00510.1544-0.00660.197151.3688-15.5573-0.8437
36.2632-3.6784-0.66334.34670.67973.20350.02860.51620.4758-0.4543-0.01570.0414-0.23440.00420.00850.2152-0.0484-0.03330.19220.04380.257253.1268-5.3934-8.6934
42.18761.09911.5694.30085.44256.9361-0.00720.1245-0.0062-0.27090.0271-0.1209-0.1011-0.0568-0.06970.159-0.01640.00340.15050.01190.168463.8716-6.0932-5.184
54.77380.7624-0.51592.3271-0.67963.74640.0107-0.1139-0.08930.0702-0.1427-0.26970.04130.29720.1320.1147-0.011-0.01380.1455-0.00930.153271.9764-12.60386.4048
60.81220.233-0.32041.591-1.06152.3945-0.1438-0.5346-0.16850.45070.11340.24040.06260.0481-0.15120.25960.05320.08290.27460.0680.1761.1551-15.033731.4844
73.50430.97110.01850.3479-0.45572.70040.1175-0.2538-0.40830.52060.32270.6532-0.0612-0.1985-0.00470.31690.01140.03240.1840.13270.349867.6338-35.679928.1723
80.9942-0.32810.78420.7742-0.5841.4070.047-0.2828-0.19680.26940.12460.2650.1125-0.0685-0.12750.24570.00390.04120.21120.08740.210667.7914-28.909631.787
91.9326-0.15360.78791.8162-0.42941.46120.1096-0.0935-0.14340.08130.05170.30840.0722-0.1-0.15620.2064-0.00870.01420.19280.06080.211761.5265-25.018823.8324
103.4222-1.57062.07221.6242-0.42841.5564-0.0293-0.0696-0.00510.2829-0.5157-0.6493-0.04221.06590.38420.2168-0.0006-0.07170.48120.2060.29781.4492-25.290127.1467
112.2436-1.11131.19753.4510.71163.6646-0.009-0.8341-0.48730.7855-0.0931-0.2444-0.56650.39350.14110.4072-0.0898-0.04130.35750.11520.203176.2454-22.92435.1025
128.93672.5634-7.13965.4768-5.228.4634-0.1483-0.45180.22280.56490.0221-0.1515-0.2910.01150.1340.2681-0.0157-0.04910.2287-0.00460.120872.719-12.765631.7147
131.67110.0260.56735.30270.30974.1583-0.0787-0.12180.32010.0961-0.08310.2787-0.2249-0.09440.18120.17720.00410.02270.11770.01950.132464.1308-6.91420.1714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 41 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 42 THROUGH 130 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 131 THROUGH 148 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 149 THROUGH 160 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 161 THROUGH 180 )A0
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 2 THROUGH 37 )B0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 38 THROUGH 53 )B0
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 54 THROUGH 82 )B0
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 83 THROUGH 117 )B0
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 118 THROUGH 130 )B0
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 131 THROUGH 148 )B0
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 149 THROUGH 160 )B0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 161 THROUGH 180 )B0

+
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