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

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Basic information

Entry
Database: PDB / ID: 5nfm
TitleCrystal structure of YrbA from Sinorhizobium meliloti in complex with copper.
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
COPPER (II) ION / : / YrbA / :
Similarity search - Component
Biological speciesSinorhizobium meliloti 2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.8 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 1.1Nov 4, 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.ptnr2_auth_seq_id
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YrbA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0263
Polymers7,9551
Non-polymers702
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Monomeric, gel filtration, Monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-9 kcal/mol
Surface area4650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.752, 32.159, 62.575
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 2011 (bacteria) / Gene: SM2011_c00487 / Production host: Escherichia coli (E. coli) / References: UniProt: M4MWA0, UniProt: A0A452CS62*PLUS
#2: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.94 Å3/Da / Density % sol: 36.75 %
Crystal growTemperature: 277 K / Method: microbatch
Details: 0.7 M lithium sulfate 0.02 M copper acetate 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: 0.722307 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.722307 Å / Relative weight: 1
ReflectionResolution: 0.8→32.16 Å / Num. all: 465091 / Num. obs: 66196 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.034 / Rrim(I) all: 0.091 / Net I/σ(I): 15
Reflection shellResolution: 0.8→0.81 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 21702 / Num. unique all: 3201 / CC1/2: 0.727 / Rpim(I) all: 0.352 / Rrim(I) all: 0.927 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NFK

5nfk


Resolution: 0.8→22.425 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 11.44
RfactorNum. reflection% reflection
Rfree0.132 3301 4.99 %
Rwork0.1217 --
obs0.1222 66112 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.8→22.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms556 0 2 150 708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.032594
X-RAY DIFFRACTIONf_angle_d0.898790
X-RAY DIFFRACTIONf_dihedral_angle_d16.425220
X-RAY DIFFRACTIONf_chiral_restr0.08386
X-RAY DIFFRACTIONf_plane_restr0.005108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.8004-0.81180.24971470.21632530X-RAY DIFFRACTION99
0.8118-0.82390.20361050.19682636X-RAY DIFFRACTION100
0.8239-0.83680.23171340.18922592X-RAY DIFFRACTION100
0.8368-0.85050.19391420.18812565X-RAY DIFFRACTION100
0.8505-0.86520.18481450.17032577X-RAY DIFFRACTION100
0.8652-0.88090.17221400.15562593X-RAY DIFFRACTION100
0.8809-0.89790.15051420.15022567X-RAY DIFFRACTION100
0.8979-0.91620.18151540.15222589X-RAY DIFFRACTION100
0.9162-0.93610.16211420.13262590X-RAY DIFFRACTION100
0.9361-0.95790.15391300.1192587X-RAY DIFFRACTION100
0.9579-0.98190.15141430.12162581X-RAY DIFFRACTION100
0.9819-1.00840.11641310.1152635X-RAY DIFFRACTION100
1.0084-1.03810.11941360.11132610X-RAY DIFFRACTION100
1.0381-1.07160.09651160.10112585X-RAY DIFFRACTION100
1.0716-1.10990.0911160.09772661X-RAY DIFFRACTION100
1.1099-1.15430.12361430.09232590X-RAY DIFFRACTION100
1.1543-1.20690.11921210.09812629X-RAY DIFFRACTION100
1.2069-1.27050.10561830.10242585X-RAY DIFFRACTION100
1.2705-1.35010.11421340.10092644X-RAY DIFFRACTION100
1.3501-1.45430.11551520.11012615X-RAY DIFFRACTION100
1.4543-1.60060.11371460.11382652X-RAY DIFFRACTION100
1.6006-1.83210.12941600.11942650X-RAY DIFFRACTION100
1.8321-2.30790.10381280.11082715X-RAY DIFFRACTION100
2.3079-22.43420.13831110.12542833X-RAY DIFFRACTION99

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