[English] 日本語
Yorodumi
- PDB-7kq2: 1.98 A resolution crystal structure of Group A Streptococcus H111... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kq2
Title1.98 A resolution crystal structure of Group A Streptococcus H111A HupZ-V5-His6
ComponentsHupZ
KeywordsOXIDOREDUCTASE / heme degradation / heme binding protein / enzyme
Function / homologyPyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / FMN-binding split barrel / Pyridoxamine 5'-phosphate oxidase N-terminal domain-containing protein
Function and homology information
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.981 Å
AuthorsTraore, E. / Li, J. / Liu, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01CA247379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
CitationJournal: Molecules / Year: 2021
Title: Heme Binding to HupZ with a C-Terminal Tag from Group A Streptococcus.
Authors: Traore, E.S. / Li, J. / Chiura, T. / Geng, J. / Sachla, A.J. / Yoshimoto, F. / Eichenbaum, Z. / Davis, I. / Mak, P.J. / Liu, A.
History
DepositionNov 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HupZ
B: HupZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,63210
Polymers36,8722
Non-polymers7618
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, DIMER
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-109 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.898, 54.898, 333.279
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein HupZ / Pyridoxamine 5'-phosphate oxidase


Mass: 18435.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Gene: MGAS10270_SPY0711 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9A0B9*PLUS, pyridoxal 5'-phosphate synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 5 mg/mL protein, 0.1 M citric acid, 1.3 M ammonium sulfate, pH 3.4
PH range: 3-4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 22490 / % possible obs: 99.9 % / Redundancy: 29.4 % / Biso Wilson estimate: 30.44 Å2 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.032 / Rrim(I) all: 0.174 / Χ2: 1.024 / Net I/σ(I): 3.6 / Num. measured all: 661695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.97-2320.97210580.9060.170.9870.492100
2-2.0430.80.92611010.9250.1640.9410.516100
2.04-2.0830.30.79410720.920.1430.8070.955100
2.08-2.12300.76110970.9530.1370.7740.55799.8
2.12-2.1727.40.56810900.9540.1080.5790.58999.9
2.17-2.2229.50.5310690.9670.0980.5390.631100
2.22-2.2729.30.76811130.9270.1390.7813.591100
2.27-2.3431.70.42910660.9820.0770.4360.638100
2.34-2.4310.36311150.9830.0660.370.691100
2.4-2.4830.50.33411070.9860.0610.340.693100
2.48-2.5730.20.30210980.9860.0560.3080.752100
2.57-2.6729.80.2811080.9890.0510.2850.844100
2.67-2.826.60.23311190.9880.0460.2370.86199.7
2.8-2.9429.20.19510990.9910.0370.1980.936100
2.94-3.1330.40.16711330.9950.0310.171.064100
3.13-3.3729.60.14711510.9960.0280.1491.163100
3.37-3.7128.40.17511490.9930.0330.1782.059100
3.71-4.2424.60.12311680.9970.0250.1251.54599.7
4.24-5.3529.90.09812090.9980.0180.11.035100
5.35-5028.10.08413680.9980.0160.0860.96899.8

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.9refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5ESC

5esc


Resolution: 1.981→38.706 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.5 / Phase error: 21.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 2000 9.36 %
Rwork0.1931 19373 -
obs0.1965 21373 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.74 Å2 / Biso mean: 34.8667 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 1.981→38.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 42 119 2054
Biso mean--48.51 38.24 -
Num. residues----238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071968
X-RAY DIFFRACTIONf_angle_d1.0312653
X-RAY DIFFRACTIONf_chiral_restr0.04284
X-RAY DIFFRACTIONf_plane_restr0.004343
X-RAY DIFFRACTIONf_dihedral_angle_d13.933745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.981-2.03050.29931340.2294130494
2.0305-2.08540.2951320.2234127894
2.0854-2.14670.22951350.2119131395
2.1467-2.2160.21721400.2013134797
2.216-2.29520.33151270.2644122187
2.2952-2.38710.27321420.1965137598
2.3871-2.49570.25511410.2124136998
2.4957-2.62720.33741400.2065136098
2.6272-2.79180.27091440.217140099
2.7918-3.00730.24931450.204140099
3.0073-3.30980.22061470.1883142999
3.3098-3.78840.19961500.1668144499
3.7884-4.77150.17291540.1543149799
4.7715-38.7060.20721690.20271636100

+
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