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- PDB-4ofo: Crystal structure of YntA from Yersinia pestis, unliganded form -

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Basic information

Entry
Database: PDB / ID: 4ofo
TitleCrystal structure of YntA from Yersinia pestis, unliganded form
ComponentsExtracytoplasmic Nickel-Binding Protein YpYntA
KeywordsTRANSPORT PROTEIN / Nickel import / Periplasmic / ABC-type importer / extracytoplasmic nickel-binding protein
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space
Similarity search - Function
Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Solute-binding protein / Solute-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLebrette, H. / Cavazza, C.
CitationJournal: Structure / Year: 2014
Title: Promiscuous nickel import in human pathogens: structure, thermodynamics, and evolution of extracytoplasmic nickel-binding proteins.
Authors: Lebrette, H. / Brochier-Armanet, C. / Zambelli, B. / de Reuse, H. / Borezee-Durant, E. / Ciurli, S. / Cavazza, C.
History
DepositionJan 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracytoplasmic Nickel-Binding Protein YpYntA
B: Extracytoplasmic Nickel-Binding Protein YpYntA
C: Extracytoplasmic Nickel-Binding Protein YpYntA
D: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,2498
Polymers220,0144
Non-polymers2354
Water48627
1
A: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0622
Polymers55,0041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0622
Polymers55,0041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0622
Polymers55,0041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0622
Polymers55,0041
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.230, 144.690, 149.190
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
Extracytoplasmic Nickel-Binding Protein YpYntA / Putative substrate-binding periplasmic protein of ABC transporter / YpYntA


Mass: 55003.547 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: oppA4, y1231, YP_2461, YPO2660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CJS8, UniProt: A0A2U2H355*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17 % PEG 6K, 50 mM HEPES pH 7.5 + NiCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→47.932 Å / Num. all: 44590 / Num. obs: 44529 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rsym value: 0.126 / Net I/σ(I): 12.61
Reflection shellResolution: 3→3.1 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 2.68 / Rsym value: 0.723 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RY3

3ry3


Resolution: 3→47.932 Å / σ(F): 1.36 / Phase error: 23.14 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2243 2275 5.11 %
Rwork0.1943 --
obs0.1955 44529 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15476 0 4 27 15507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115936
X-RAY DIFFRACTIONf_angle_d1.12821764
X-RAY DIFFRACTIONf_dihedral_angle_d12.4445680
X-RAY DIFFRACTIONf_chiral_restr0.0372320
X-RAY DIFFRACTIONf_plane_restr0.0052832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06530.33841380.27722618X-RAY DIFFRACTION95
3.0653-3.13660.31271360.26262585X-RAY DIFFRACTION95
3.1366-3.21510.30551380.24632612X-RAY DIFFRACTION95
3.2151-3.3020.24861380.24152621X-RAY DIFFRACTION95
3.302-3.39910.23971380.22592626X-RAY DIFFRACTION95
3.3991-3.50880.26561360.21372593X-RAY DIFFRACTION95
3.5088-3.63410.24411380.2142616X-RAY DIFFRACTION95
3.6341-3.77960.22341380.19922620X-RAY DIFFRACTION95
3.7796-3.95150.2551380.19322613X-RAY DIFFRACTION95
3.9515-4.15970.2281380.1872640X-RAY DIFFRACTION95
4.1597-4.42020.19451400.17352648X-RAY DIFFRACTION95
4.4202-4.76120.19451380.16382629X-RAY DIFFRACTION95
4.7612-5.23970.19871410.16132669X-RAY DIFFRACTION95
5.2397-5.99660.24211410.17882683X-RAY DIFFRACTION95
5.9966-7.55010.20881420.18432700X-RAY DIFFRACTION95
7.5501-47.03550.16771490.17912821X-RAY DIFFRACTION94
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)
13.3347-0.37390.12542.78850.21792.2543-0.0153-0.093-0.0080.20730.1555-0.7339-0.13260.2334-0.17030.41950.0436-0.02320.3566-0.0210.601745.325726.5829177.6356
22.3769-0.92240.52911.98690.12471.8519-0.0423-0.464-0.25190.52780.1441-0.6570.1556-0.0049-0.0780.48510.0407-0.14460.35160.07370.681744.193123.5178182.8513
32.8308-2.4463-0.012.1941-0.16330.2589-0.2649-0.35780.29030.310.4669-1.0860.36510.6349-0.280.58180.0485-0.28810.7128-0.18411.31264.242238.2356190.6377
41.394-0.62930.32683.76131.021.01540.1302-0.13550.13830.0720.1356-1.3959-0.04180.1109-0.16960.4214-0.067-0.05310.3099-0.03910.877947.518354.2661190.2844
53.50632.02090.042.46210.27681.793-0.13070.0145-0.3588-0.1330.0827-0.26420.1694-0.29350.04340.4095-0.04130.02840.3551-0.01820.25519.687530.154198.3861
60.61490.4405-0.43730.9746-0.46812.17130.0520.09160.04190.07620.0940.1593-0.0582-0.4711-0.11860.2699-0.00750.00720.39630.03890.29721.799938.7514171.2266
72.11130.9249-1.77880.787-0.10252.7597-0.1475-0.0582-0.19310.10710.0367-0.02220.19230.19910.03410.49270.01220.0610.4370.01480.460327.793483.9055150.1275
83.11080.6472-1.67131.0272-0.77081.77970.0216-0.40240.09240.2026-0.01310.0533-0.21210.22380.01180.4901-0.03470.02260.3809-0.01530.301833.446387.5108152.2773
92.0276-1.7118-1.87041.50521.69521.8999-0.15210.0095-0.40510.3368-0.15860.41850.1877-0.57120.26990.40090.04490.06240.48110.02240.402611.551670.7535153.4865
100.75920.0257-0.15022.4061-0.0250.7934-0.07-0.0088-0.0493-0.03120.05610.1322-0.0177-0.00860.00520.2526-0.00190.00150.303-0.0220.17126.277257.5153141.8405
112.96880.16761.54711.2674-0.1562.7274-0.3247-0.4520.7120.1344-0.1444-0.2267-0.24380.21190.3780.3867-0.0165-0.05750.741-0.11870.750366.809570.0973159.0103
120.8049-0.54790.10981.0836-0.90671.9619-0.0320.96060.4772-0.0779-0.4766-0.5955-0.03441.14580.3790.3915-0.06840.11791.44940.32240.843372.047378.2607130.3038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 78 )
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 197 )
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 498 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 197 )
6X-RAY DIFFRACTION6chain 'B' and (resid 198 through 498 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 54 )
8X-RAY DIFFRACTION8chain 'C' and (resid 55 through 197 )
9X-RAY DIFFRACTION9chain 'C' and (resid 198 through 232 )
10X-RAY DIFFRACTION10chain 'C' and (resid 233 through 498 )
11X-RAY DIFFRACTION11chain 'D' and (resid 2 through 197 )
12X-RAY DIFFRACTION12chain 'D' and (resid 198 through 498 )

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