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- PDB-6dzx: Crystal structure of the N. meningitides methionine-binding prote... -

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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 / homology
Function and homology information


Lipoprotein NlpA family / NlpA lipoprotein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-METHIONINE / Lipoprotein
Similarity search - Component
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 1387 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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