[English] 日本語
Yorodumi
- PDB-5i01: Structure of phosphoheptose isomerase GmhA from Neisseria gonorrhoeae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i01
TitleStructure of phosphoheptose isomerase GmhA from Neisseria gonorrhoeae
ComponentsPhosphoheptose isomerase
KeywordsISOMERASE / phosphoheptose isomerase / Zn binding protein
Function / homology
Function and homology information


D-sedoheptulose-7-phosphate isomerase / D-sedoheptulose 7-phosphate isomerase activity / D-glycero-D-manno-heptose 7-phosphate biosynthetic process / carbohydrate derivative binding / carbohydrate metabolic process / zinc ion binding / cytoplasm
Similarity search - Function
Phosphoheptose isomerase / GmhA/DiaA / SIS domain / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoheptose isomerase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å
AuthorsWierzbicki, I.H. / Sikora, A.E. / Korotkov, K.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI117235 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103486 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: Microbiologyopen / Year: 2017
Title: Functional and structural studies on the Neisseria gonorrhoeae GmhA, the first enzyme in the glycero-manno-heptose biosynthesis pathways, demonstrate a critical role in lipooligosaccharide ...Title: Functional and structural studies on the Neisseria gonorrhoeae GmhA, the first enzyme in the glycero-manno-heptose biosynthesis pathways, demonstrate a critical role in lipooligosaccharide synthesis and gonococcal viability.
Authors: Wierzbicki, I.H. / Zielke, R.A. / Korotkov, K.V. / Sikora, A.E.
History
DepositionFeb 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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 / struct_conn
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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoheptose isomerase
B: Phosphoheptose isomerase
C: Phosphoheptose isomerase
D: Phosphoheptose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9538
Polymers86,6924
Non-polymers2624
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14160 Å2
ΔGint-241 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.360, 130.150, 47.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
Phosphoheptose isomerase / Sedoheptulose 7-phosphate isomerase


Mass: 21672.879 Da / Num. of mol.: 4 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: gmhA, NGO1986 / Plasmid: pRSF-NT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5F5E3, D-sedoheptulose-7-phosphate isomerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M TRIS-HCL pH 8.5, 0.2M magnesium chloride, 30% PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 13, 2015
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→85.91 Å / Num. obs: 28174 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 41.167 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.134 / Net I/σ(I): 9.34
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.37-2.431.0321.71197.8
2.43-2.50.9381.91197.5
2.5-2.570.8572.19197.5
2.57-2.650.6362.75197.2
2.65-2.740.5433.36197.4
2.74-2.830.453.76197.1
2.83-2.940.3854.29197.1
2.94-3.060.2885.59196.7
3.06-3.20.2286.61196.2
3.2-3.350.1678.3196.4
3.35-3.530.1359.91195.6
3.53-3.750.08713.41195.4
3.75-4.010.0617.25194.6
4.01-4.330.04820.19194
4.33-4.740.0424.21193.9
4.74-5.30.04122.66193.4
5.3-6.120.0519.98192.9
6.12-7.490.03722.66191.8
7.49-10.60.0232.24189.7
10.60.01831.92183.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.21 Å85.91 Å
Translation7.21 Å85.91 Å

-
Processing

Software
NameVersionClassification
XSCALENovember 3, 2014 BUILT=20141118data scaling
PHASER2.5.7phasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
XDSNovember 3, 2014data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BJZ
Resolution: 2.37→85.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.869 / SU ML: 0.239 / SU R Cruickshank DPI: 0.5474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.547 / ESU R Free: 0.296
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 1405 5 %RANDOM
Rwork0.2071 ---
obs0.2101 26786 95.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 85.76 Å2 / Biso mean: 37.172 Å2 / Biso min: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---2.2 Å20 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2.37→85.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 4 101 5516
Biso mean--54.9 32.72 -
Num. residues----733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195483
X-RAY DIFFRACTIONr_bond_other_d0.0010.025360
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9527405
X-RAY DIFFRACTIONr_angle_other_deg0.93312277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1655725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89925232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.98715938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6761532
X-RAY DIFFRACTIONr_chiral_restr0.0690.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021169
X-RAY DIFFRACTIONr_mcbond_it1.4783.542924
X-RAY DIFFRACTIONr_mcbond_other1.4773.5392923
X-RAY DIFFRACTIONr_mcangle_it2.4325.3033641
LS refinement shellResolution: 2.37→2.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 112 -
Rwork0.324 1955 -
all-2067 -
obs--97.59 %

+
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://pdbjlvh1.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