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

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Basic information

Entry
Database: PDB / ID: 6cva
TitleCrystal structure of the N. meningitides methionine-binding protein in its substrate-free conformation
ComponentsLipoprotein
KeywordsPROTEIN BINDING / substrate-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 / Lipoprotein
Function and homology information
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.559 Å
AuthorsNguyen, P.T. / Lai, J.Y. / Kaiser, J.T. / Rees, D.C.
Funding support United States, Viet Nam, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Vietnam International Education DevelopmentViet Nam
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
DepositionMar 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein


Theoretical massNumber of molelcules
Total (without water)26,9861
Polymers26,9861
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.564, 89.663, 45.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

21A-526-

HOH

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Components

#1: Protein Lipoprotein


Mass: 26985.926 Da / Num. of mol.: 1 / Fragment: residues 44-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria)
Gene: gna1946, A6J54_04155, A6L27_04980, CWI43_07600, CWI45_01195, CWI46_00955, CWI48_04325, CWI52_00775, CWI53_02070, CWI56_11320, CWI58_01890, CWI60_00490, ERS514410_01419, ERS514851_01229
Production host: Escherichia coli (E. coli) / References: UniProt: Q9JPG4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M MgCl2, 0.1M Bis-Tris pH5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.19→34.223 Å / Num. obs: 128188 / % possible obs: 95.6 % / Redundancy: 3.321 % / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.132 / Χ2: 1.069 / Net I/σ(I): 4.23 / Num. measured all: 425726 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible allCC1/2
1.19-1.222.554.8840.1517964991670456.15371
1.22-1.253.3543.9330.2431625963694294.6997.9
1.25-1.293.3853.1230.3131281940492413.71698.3
1.29-1.333.3242.5480.3929547906088883.04498.10.119
1.33-1.373.1991.9560.527387881585602.35897.10.185
1.37-1.423.4841.4730.7429359856584271.74298.40.33
1.42-1.483.4421.0841.0527786821780721.28698.20.471
1.48-1.543.3670.7951.4726125794377580.94797.70.62
1.54-1.613.1880.5772.0423420762473460.69696.40.749
1.61-1.683.4480.4442.8824592726871320.52798.10.867
1.68-1.773.4060.3213.9923081693467760.38297.70.922
1.77-1.883.3440.235.4421272657463620.27596.80.953
1.88-2.013.1520.1697.4518352613858230.20494.90.966
2.01-2.173.5320.14610.120024576256690.17398.40.978
2.17-2.383.5270.12511.618399528852170.14898.70.98
2.38-2.663.4230.10212.7416088478947000.12298.10.984
2.66-3.073.2660.08114.0213224422040490.09795.90.988
3.07-3.763.4770.06816.1112211357935120.08198.10.992
3.76-5.323.2920.0616.778790278326700.07195.90.991
5.32-34.2233.4380.05917.155199154915120.06997.60.994

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.559→34.223 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.77 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2201 2000 6.5 %
Rwork0.1881 28757 -
obs0.1902 30757 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.03 Å2 / Biso mean: 27.6846 Å2 / Biso min: 7.49 Å2
Refinement stepCycle: final / Resolution: 1.559→34.223 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 0 248 2143
Biso mean---32.69 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031937
X-RAY DIFFRACTIONf_angle_d0.6812627
X-RAY DIFFRACTIONf_chiral_restr0.047290
X-RAY DIFFRACTIONf_plane_restr0.005341
X-RAY DIFFRACTIONf_dihedral_angle_d14.3041163
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5587-1.59760.32291220.26191752187486
1.5976-1.64080.26321400.24272012215298
1.6408-1.68910.25481420.22642035217799
1.6891-1.74360.25961410.211320322173100
1.7436-1.8060.2251410.210620372178100
1.806-1.87830.27871450.214220752220100
1.8783-1.96370.27711420.206120472189100
1.9637-2.06730.20891420.19120472189100
2.0673-2.19680.2151450.181220772222100
2.1968-2.36630.2131450.17920842229100
2.3663-2.60440.2391440.181820792223100
2.6044-2.98110.20171470.181721142261100
2.9811-3.75510.20421490.172621322281100
3.7551-34.23090.19671550.178722342389100
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)
10.84840.1271-0.04050.5535-0.11310.50840.034-0.01010.3225-0.01780.00270.0127-0.06590.07590.04990.1188-0.0090.00350.10580.01140.187336.634531.46642.7999
21.10060.3859-0.21070.69860.18640.4150.0717-0.1867-0.0440.1167-0.0329-0.03340.12430.01440.00160.1120.0032-0.00950.11070.01280.082634.301418.922247.2766
31.19330.28120.0291.1139-0.79581.4144-0.04760.3156-0.2813-0.2374-0.0104-0.06930.19730.1429-0.28860.17790.0072-0.01130.1829-0.05250.149239.90884.282527.0576
40.98710.51-0.5580.94080.29760.82270.01050.19760.2833-0.1103-0.00890.1996-0.0783-0.2473-0.30230.10150.0076-0.0120.14810.03880.125827.043926.49437.1409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 44 through 89 )A44 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 126 )A90 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 238 )A127 - 238
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 284 )A239 - 284

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