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- PDB-6nio: Crystal Structure of the Molybdate Transporter Periplasmic Protei... -

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Basic information

Entry
Database: PDB / ID: 6nio
TitleCrystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis
ComponentsMolybdate ABC transporter substrate-binding protein
KeywordsTRANSPORT PROTEIN / Periplasmic Protein ModA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / ACETIC ACID / FORMIC ACID / :
Function and homology information
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.37 Å
AuthorsKim, Y. / Joachimiak, G. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Molybdate Transporter Periplasmic Protein ModA from Yersinia pestis
Authors: Kim, Y. / Joachimiak, G. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdate ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0284
Polymers25,7141
Non-polymers3133
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint1 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.922, 54.305, 69.785
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Molybdate ABC transporter substrate-binding protein / Molybdate transporter periplasmic protein / Molybdate-binding periplasmic protein


Mass: 25714.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: modA, modA2, YP_1015, C6P89_14820, NCTC144_03853 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S9PEQ7
#2: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.93 Å3/Da / Density % sol: 36.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.1 M CHES pH 9.5, 1.0 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.37→50 Å / Num. obs: 41969 / % possible obs: 99.8 % / Redundancy: 11.9 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 35.9
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.687 / Mean I/σ(I) obs: 3.25 / Num. unique obs: 2078 / CC1/2: 0.883 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.37→41.657 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.39
RfactorNum. reflection% reflection
Rfree0.1788 2082 4.97 %
Rwork0.1602 --
obs0.1611 41907 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.37→41.657 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 20 191 1986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131918
X-RAY DIFFRACTIONf_angle_d1.2342617
X-RAY DIFFRACTIONf_dihedral_angle_d18.006720
X-RAY DIFFRACTIONf_chiral_restr0.103295
X-RAY DIFFRACTIONf_plane_restr0.009342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3705-1.40240.2231330.18222509X-RAY DIFFRACTION95
1.4024-1.43740.20811440.16262595X-RAY DIFFRACTION100
1.4374-1.47630.2061300.15242624X-RAY DIFFRACTION99
1.4763-1.51970.18661360.13932633X-RAY DIFFRACTION100
1.5197-1.56880.18931140.13152655X-RAY DIFFRACTION100
1.5688-1.62490.17381440.132645X-RAY DIFFRACTION100
1.6249-1.68990.17461480.13542603X-RAY DIFFRACTION100
1.6899-1.76680.19141600.13552627X-RAY DIFFRACTION100
1.7668-1.860.18831290.14112662X-RAY DIFFRACTION100
1.86-1.97650.16991150.14552680X-RAY DIFFRACTION100
1.9765-2.12910.17291460.14822655X-RAY DIFFRACTION100
2.1291-2.34340.20021290.15392700X-RAY DIFFRACTION100
2.3434-2.68240.19781450.17522695X-RAY DIFFRACTION100
2.6824-3.37930.17651660.18222683X-RAY DIFFRACTION100
3.3793-41.67590.16151430.16262859X-RAY DIFFRACTION100

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