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- PDB-5anp: CRYSTAL STRUCTURE OF THE BA41 PROTEIN FROM BIZIONIA ARGENTINENSIS -

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Basic information

Entry
Database: PDB / ID: 5anp
TitleCRYSTAL STRUCTURE OF THE BA41 PROTEIN FROM BIZIONIA ARGENTINENSIS
ComponentsBA41
KeywordsUNKNOWN FUNCTION / ANTARCTIC BACTERIA / BA41
Function / homologyDiaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / membrane / Alpha Beta / TPM domain-containing protein
Function and homology information
Biological speciesBIZIONIA ARGENTINENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsOtero, L.H. / Cerutti, M.L. / Goldbaum, F.A. / Klinke, S.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural and functional characterization of a cold adapted TPM-domain with ATPase/ADPase activity.
Authors: Cerutti, M.L. / Otero, L.H. / Smal, C. / Pellizza, L. / Goldbaum, F.A. / Klinke, S. / Aran, M.
History
DepositionSep 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BA41
B: BA41


Theoretical massNumber of molelcules
Total (without water)58,3242
Polymers58,3242
Non-polymers00
Water5,224290
1
A: BA41


Theoretical massNumber of molelcules
Total (without water)29,1621
Polymers29,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BA41


Theoretical massNumber of molelcules
Total (without water)29,1621
Polymers29,1621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.623, 58.135, 60.198
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BA41


Mass: 29161.879 Da / Num. of mol.: 2 / Fragment: TPM DOMAIN, UNP RESIDUES 29-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BIZIONIA ARGENTINENSIS (bacteria) / Strain: JUB59 / Plasmid: PDEST527 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: G2EA44
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.53 % / Description: NONE
Crystal growpH: 6.1
Details: 23% PEG 5000 MME, 2% PEG 400, 0.1M IMIDAZOLE PH 6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.82656
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.4→34.43 Å / Num. obs: 46549 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Biso Wilson estimate: 13.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
MrBUMPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2KW7

2kw7


Resolution: 1.4→34.43 Å / Cor.coef. Fo:Fc: 0.9569 / Cor.coef. Fo:Fc free: 0.9535 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.067 / SU Rfree Blow DPI: 0.063 / SU Rfree Cruickshank DPI: 0.062
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 2320 4.99 %RANDOM
Rwork0.1755 ---
obs0.1761 46527 99.39 %-
Displacement parametersBiso mean: 17.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.5389 Å20 Å2-0.4804 Å2
2---1.5374 Å20 Å2
3----1.0016 Å2
Refine analyzeLuzzati coordinate error obs: 0.154 Å
Refinement stepCycle: LAST / Resolution: 1.4→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 290 2515
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012264HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033071HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d785SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes318HARMONIC5
X-RAY DIFFRACTIONt_it2264HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3016SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2234 165 4.85 %
Rwork0.2181 3238 -
all0.2184 3403 -
obs--99.39 %

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