[English] 日本語
Yorodumi
- PDB-6dzx: Crystal structure of the N. meningitides methionine-binding prote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dzx
TitleCrystal structure of the N. meningitides methionine-binding protein in its D-methionine bound conformation.
ComponentsLipoprotein
KeywordsPROTEIN BINDING / methionine-binding protein
Function / homologyLipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / membrane / Alpha Beta / D-METHIONINE / Lipoprotein
Function and homology information
Biological speciesNeisseria meningitidis alpha153 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.678 Å
AuthorsNguyen, P.T. / Lai, J.Y. / Kaiser, J.T. / Rees, D.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Protein Sci. / Year: 2019
Title: Structures of the Neisseria meningitides methionine-binding protein MetQ in substrate-free form and bound to l- and d-methionine isomers.
Authors: Nguyen, P.T. / Lai, J.Y. / Kaiser, J.T. / Rees, D.C.
History
DepositionJul 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipoprotein
B: Lipoprotein
C: Lipoprotein
D: Lipoprotein
E: Lipoprotein
F: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,23212
Polymers165,3376
Non-polymers8956
Water24,9871387
1
A: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7052
Polymers27,5561
Non-polymers1491
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.663, 87.933, 91.639
Angle α, β, γ (deg.)114.830, 104.120, 105.390
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and resid 44 through 283)
31(chain C and resid 44 through 283)
41(chain D and resid 44 through 283)
51(chain E and resid 44 through 283)
61chain F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1MEDMEDchain AAA - G44 - 10014
2GLUGLU(chain B and resid 44 through 283)BB44 - 2834 - 243
3GLUGLU(chain C and resid 44 through 283)CC44 - 2834 - 243
4GLUGLU(chain D and resid 44 through 283)DD44 - 2834 - 243
5GLUGLU(chain E and resid 44 through 283)EE44 - 2834 - 243
6MEDMEDchain FFF - L44 - 10014

-
Components

#1: Protein
Lipoprotein /


Mass: 27556.111 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis alpha153 (bacteria)
Gene: sfbA, NME_0028 / Production host: Escherichia coli (E. coli) / References: UniProt: C6S9R8
#2: Chemical
ChemComp-MED / D-METHIONINE / Methionine


Type: D-peptide linking / Mass: 149.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1387 / 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: 3.16 Å3/Da / Density % sol: 61.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: contains 2.3M (NH4)2SO4, 0.1M sodium acetate pH 5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97964 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 1.68→39.67 Å / Num. obs: 219506 / % possible obs: 96.4 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.036 / Rrim(I) all: 0.137 / Net I/σ(I): 10.5 / Num. measured all: 3103914 / Scaling rejects: 87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.68-1.7113.94.454143999103950.2941.2494.6350.792.2
9.19-39.6715.20.0522080113670.9990.0140.0544298.3

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.678→39.669 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2012 11054 5.06 %
Rwork0.1765 207373 -
obs0.1777 218427 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 206.12 Å2 / Biso mean: 38.2686 Å2 / Biso min: 19.08 Å2
Refinement stepCycle: final / Resolution: 1.678→39.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11400 0 114 1387 12901
Biso mean--31.1 42.69 -
Num. residues----1445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111700
X-RAY DIFFRACTIONf_angle_d1.10815855
X-RAY DIFFRACTIONf_chiral_restr0.0731750
X-RAY DIFFRACTIONf_plane_restr0.0082057
X-RAY DIFFRACTIONf_dihedral_angle_d15.5647027
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8780X-RAY DIFFRACTION6.517TORSIONAL
12B8780X-RAY DIFFRACTION6.517TORSIONAL
13C8780X-RAY DIFFRACTION6.517TORSIONAL
14D8780X-RAY DIFFRACTION6.517TORSIONAL
15E8780X-RAY DIFFRACTION6.517TORSIONAL
16F8780X-RAY DIFFRACTION6.517TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6784-1.69750.36673010.36566394669587
1.6975-1.71740.38023220.34756667698993
1.7174-1.73840.34223310.33366791712294
1.7384-1.76040.34253800.31616849722995
1.7604-1.78360.33273700.31266718708895
1.7836-1.8080.34243600.29936886724695
1.808-1.83380.31393840.28476919730396
1.8338-1.86120.26293680.26376891725996
1.8612-1.89030.25373430.24656947729096
1.8903-1.92130.26773900.23326928731896
1.9213-1.95440.25684130.22496916732996
1.9544-1.98990.25273580.21346954731296
1.9899-2.02820.22583530.2026870722397
2.0282-2.06960.21554040.1966956736097
2.0696-2.11460.22073920.1926959735197
2.1146-2.16380.2263710.19316965733697
2.1638-2.21790.22833450.18396976732197
2.2179-2.27780.19323490.17037013736297
2.2778-2.34490.20443900.16457009739997
2.3449-2.42050.20224390.16666956739597
2.4205-2.5070.18643830.15966958734197
2.507-2.60740.20063710.16797023739498
2.6074-2.7260.19883490.16836998734797
2.726-2.86970.19523520.16897050740298
2.8697-3.04950.21153830.17177034741798
3.0495-3.28480.19623830.1697010739398
3.2848-3.61520.16663580.15576998735697
3.6152-4.13780.15363270.13826962728996
4.1378-5.21140.14993730.12896995736897
5.2114-39.68050.19974120.18656781719395

+
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