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- PDB-4ofl: Crystal structure of YntA from Yersinia pestis in complex with Ni... -

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Basic information

Entry
Database: PDB / ID: 4ofl
TitleCrystal structure of YntA from Yersinia pestis in complex with Ni(L-His)2
ComponentsExtracytoplasmic Nickel-Binding Protein YpYntA
KeywordsTRANSPORT PROTEIN / Nickel import / Periplasmic / ABC-type importer / extracytoplasmic nickel-binding protein
Function / homology
Function and homology information


ATP-binding cassette (ABC) transporter complex / transmembrane transport / 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
HISTIDINE / NICKEL (II) ION / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,7498
Polymers110,0072
Non-polymers7426
Water1,910106
1
A: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3754
Polymers55,0041
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracytoplasmic Nickel-Binding Protein YpYntA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3754
Polymers55,0041
Non-polymers3713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 213.830, 52.870
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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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.: 2
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 / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10N3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29 % PEG 10K , 50 mM Tris pH 8.5, 1 M NaCl + NiCl2 + L-His, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.7→46.451 Å / Num. all: 27904 / Num. obs: 26613 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Rsym value: 0.085 / Net I/σ(I): 10.54
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.14 / Rsym value: 0.512 / % possible all: 94.7

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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: 2.7→46.451 Å / SU ML: 0.39 / σ(F): 1.37 / Phase error: 25.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1331 5 %
Rwork0.1928 --
obs0.1948 26600 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7724 0 46 106 7876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097998
X-RAY DIFFRACTIONf_angle_d0.78310888
X-RAY DIFFRACTIONf_dihedral_angle_d12.7592848
X-RAY DIFFRACTIONf_chiral_restr0.0311160
X-RAY DIFFRACTIONf_plane_restr0.0041422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6999-2.79640.35181330.25722515X-RAY DIFFRACTION95
2.7964-2.90830.31461350.25152579X-RAY DIFFRACTION97
2.9083-3.04070.29891330.25472526X-RAY DIFFRACTION97
3.0407-3.20090.32451340.24212546X-RAY DIFFRACTION96
3.2009-3.40140.31241350.2142553X-RAY DIFFRACTION96
3.4014-3.6640.23911310.21032488X-RAY DIFFRACTION94
3.664-4.03250.20661340.17372558X-RAY DIFFRACTION97
4.0325-4.61560.17741330.1532518X-RAY DIFFRACTION95
4.6156-5.81330.18911310.16792489X-RAY DIFFRACTION94
5.8133-46.45820.20041320.17152497X-RAY DIFFRACTION93
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)
11.902-0.81561.02212.21360.26191.94870.23710.039-0.14190.2398-0.0041-0.4550.66660.4591-0.16520.67570.168-0.09720.3401-0.05170.497711.4150.705644.9806
22.3713-0.7389-1.04234.11852.60713.82080.29180.35890.2228-0.46050.2814-0.56440.55780.7816-0.56840.68230.1422-0.05980.3829-0.04010.496515.65340.329541.2867
31.71020.99430.51131.24080.16591.15490.1087-0.00120.11480.0034-0.16460.14630.10850.03270.04920.17640.04840.0070.2362-0.02090.192414.079829.006644.4543
42.36861.05931.23623.03540.48581.9226-0.07870.1868-0.2891-0.37860.03950.11740.42070.02730.01670.3011-0.04860.06430.244-0.01550.2625-0.261718.668638.4875
52.64390.49191.39463.2423-1.39262.7779-0.21520.51270.5241-0.5298-0.02230.0373-0.54380.37410.30830.7298-0.0290.01630.34660.07320.5842.560187.017526.892
61.76-0.48871.32641.93550.81914.4215-0.1730.66270.3028-0.6704-0.045-0.5812-0.57121.08470.2330.6804-0.03170.12130.55310.21250.52827.567486.763324.2907
70.56290.64480.37662.36331.18822.04080.0950.03510.2193-0.0828-0.0588-0.4462-0.16670.0191-0.01960.23480.04270.0250.25560.05660.46962.191558.901425.8296
81.88360.550.79723.00641.30612.28640.092-0.12890.38550.3517-0.0346-0.0456-0.27350.0486-0.09020.3516-0.0265-0.00630.231-0.02490.42972.840369.839541.2226
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 455 )
4X-RAY DIFFRACTION4chain 'A' and (resid 456 through 498 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 115 )
6X-RAY DIFFRACTION6chain 'B' and (resid 116 through 152 )
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 455 )
8X-RAY DIFFRACTION8chain 'B' and (resid 456 through 498 )

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