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- PDB-5nfk: Crystal structure of YrbA from Sinorhizobium meliloti in complex ... -

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Basic information

Entry
Database: PDB / ID: 5nfk
TitleCrystal structure of YrbA from Sinorhizobium meliloti in complex with nickel.
ComponentsYrbA
KeywordsLIGASE / BolA / YrbA / histidyl ligation
Function / homology
Function and homology information


: / BolA-like / BolA protein / BolA-like superfamily / BolA-like protein / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / NICKEL (II) ION / YrbA / :
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.98 Å
AuthorsRoret, T. / Didierjean, C.
CitationJournal: Biosci.Rep. / Year: 2020
Title: Sinorhizobium meliloti YrbA binds divalent metal cations using two conserved histidines.
Authors: Roret, T. / Alloing, G. / Girardet, J.M. / Perrot, T. / Dhalleine, T. / Couturier, J. / Frendo, P. / Didierjean, C. / Rouhier, N.
History
DepositionMar 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Derived calculations / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: YrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0213
Polymers7,9551
Non-polymers662
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Monomeric, gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.887, 31.917, 62.833
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 YrbA


Mass: 7955.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (strain Sm2011 / Rm2011 / 2011) (bacteria)
Gene: SM2011_c00487 / Production host: Escherichia coli (E. coli) / References: UniProt: M4MWA0, UniProt: A0A452CS62*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 1.95 Å3/Da / Density % sol: 36.81 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 1.0 M lithium sulfate 0.01 M nickel chloride 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.485952,1.486573,1.482608,0.979993
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4859521
21.4865731
31.4826081
40.9799931
ReflectionResolution: 0.98→31.92 Å / Num. obs: 35397 / % possible obs: 97.2 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.023 / Rrim(I) all: 0.077 / Net I/σ(I): 22.5
Reflection shellResolution: 0.98→1.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4201 / CC1/2: 0.82 / Rpim(I) all: 0.236 / Rrim(I) all: 0.433 / % possible all: 81.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: MAD / Resolution: 0.98→31.416 Å / SU ML: 0.04 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 9.02
RfactorNum. reflection% reflection
Rfree0.1134 1771 5.01 %
Rwork0.1013 --
obs0.1019 35335 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.98→31.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms548 0 2 112 662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009634
X-RAY DIFFRACTIONf_angle_d1.372866
X-RAY DIFFRACTIONf_dihedral_angle_d12.042248
X-RAY DIFFRACTIONf_chiral_restr0.08792
X-RAY DIFFRACTIONf_plane_restr0.006121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-1.00650.2287950.19721888X-RAY DIFFRACTION72
1.0065-1.03610.17651200.14172349X-RAY DIFFRACTION90
1.0361-1.06960.12741450.11382589X-RAY DIFFRACTION99
1.0696-1.10780.0971440.08782612X-RAY DIFFRACTION100
1.1078-1.15220.12611420.07822609X-RAY DIFFRACTION100
1.1522-1.20460.09321440.08022641X-RAY DIFFRACTION100
1.2046-1.26810.09021400.07652633X-RAY DIFFRACTION100
1.2681-1.34760.09561280.07582668X-RAY DIFFRACTION100
1.3476-1.45160.09921400.0822659X-RAY DIFFRACTION100
1.4516-1.59770.09761480.0882660X-RAY DIFFRACTION100
1.5977-1.82880.10461360.09272682X-RAY DIFFRACTION100
1.8288-2.3040.10831350.09692720X-RAY DIFFRACTION100
2.304-31.43260.12311540.12422854X-RAY DIFFRACTION100

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