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- PDB-4oa3: Crystal structure of the BA42 protein from BIZIONIA ARGENTINENSIS -

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Basic information

Entry
Database: PDB / ID: 4oa3
TitleCrystal structure of the BA42 protein from BIZIONIA ARGENTINENSIS
ComponentsPROTEIN BA42
KeywordsUNKNOWN FUNCTION / BA42
Function / homologyDiaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / membrane / metal ion binding / Alpha Beta / TPM domain-containing protein
Function and homology information
Biological speciesBizionia argentinensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsOtero, L.H. / Klinke, S. / Aran, M. / Pellizza, L. / Goldbaum, F.A. / Cicero, D.
CitationJournal: Proteins / Year: 2014
Title: Solution and crystal structure of BA42, a protein from the Antarctic bacterium Bizionia argentinensis comprised of a stand-alone TPM domain.
Authors: Aran, M. / Smal, C. / Pellizza, L. / Gallo, M. / Otero, L.H. / Klinke, S. / Goldbaum, F.A. / Ithurralde, E.R. / Bercovich, A. / Mac Cormack, W.P. / Turjanski, A.G. / Cicero, D.O.
History
DepositionJan 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 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_ref_seq_dif / 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_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.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_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_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_ref_seq_dif.details / _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: PROTEIN BA42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6363
Polymers16,5561
Non-polymers802
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.920, 39.620, 106.970
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 PROTEIN BA42


Mass: 16555.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bizionia argentinensis (bacteria) / Strain: JUB59 / Gene: BZARG_1551 / Plasmid: PDEST527 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G2EA45
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG 2000 MME, 0.1M MES pH 6.5, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: Channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. all: 27591 / Num. obs: 27591 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.31 % / Biso Wilson estimate: 19.56 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 16.01
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 4.35 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 1.99 / Num. unique all: 4307 / Rsym value: 0.695 / % possible all: 96.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
AMoREphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2LT2

2lt2


Resolution: 1.39→30.59 Å / Cor.coef. Fo:Fc: 0.9587 / Cor.coef. Fo:Fc free: 0.9423 / SU R Cruickshank DPI: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2048 1380 5 %RANDOM
Rwork0.1745 ---
all0.176 27591 --
obs0.176 27591 98.02 %-
Displacement parametersBiso mean: 23.53 Å2
Baniso -1Baniso -2Baniso -3
1-1.0227 Å20 Å20 Å2
2---5.4839 Å20 Å2
3---4.4611 Å2
Refine analyzeLuzzati coordinate error obs: 0.161 Å
Refinement stepCycle: LAST / Resolution: 1.39→30.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 2 169 1280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012293HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054150HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d522SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes348HARMONIC5
X-RAY DIFFRACTIONt_it2293HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.12
X-RAY DIFFRACTIONt_other_torsion15.12
X-RAY DIFFRACTIONt_chiral_improper_torsion158SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2768SEMIHARMONIC4
LS refinement shellResolution: 1.39→1.44 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2657 143 5.14 %
Rwork0.223 2638 -
all0.2253 2781 -
obs-2781 98.02 %

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