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- PDB-2qee: Crystal structure of putative amidohydrolase BH0493 from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 2qee
TitleCrystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125
ComponentsBH0493 protein
KeywordsHYDROLASE / amidohydrolase / BH0493 / Bacillus halodurans / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyuronate isomerase, domain 2, chain A / uronate isomerase, domain 2, chain A / Metal-dependent hydrolase / Orthogonal Bundle / Mainly Alpha / metal ion binding / BH0493 protein
Function and homology information
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMalashkevich, V.N. / Toro, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of putative amidohydrolase BH0493 from Bacillus halodurans C-125.
Authors: Malashkevich, V.N. / Toro, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: 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: BH0493 protein
B: BH0493 protein
C: BH0493 protein
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)616,11544
Polymers614,66512
Non-polymers1,44932
Water88,4364909
1
A: BH0493 protein
B: BH0493 protein
C: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,02911
Polymers153,6663
Non-polymers3628
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-165 kcal/mol
Surface area41690 Å2
MethodPISA
2
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,02911
Polymers153,6663
Non-polymers3628
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12590 Å2
ΔGint-166 kcal/mol
Surface area42190 Å2
MethodPISA
3
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,02911
Polymers153,6663
Non-polymers3628
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12620 Å2
ΔGint-165 kcal/mol
Surface area41910 Å2
MethodPISA
4
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,02911
Polymers153,6663
Non-polymers3628
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12580 Å2
ΔGint-166 kcal/mol
Surface area41870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.995, 122.208, 127.582
Angle α, β, γ (deg.)78.85, 78.95, 80.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BH0493 protein


Mass: 51222.117 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans C-125 (bacteria) / Species: Bacillus halodurans / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: BH0493 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KFI6
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4909 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris pH 6.5, 45% PPG P 400 (INDEX E10), VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 8, 2007 / Details: SGX-CAT
RadiationMonochromator: SGX-CAT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 759838 / % possible obs: 88.5 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.044 / Χ2: 1.074 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.711.50.384421801.14549.1
1.71-1.781.90.448727880.97884.8
1.78-1.862.10.338762021.03388.8
1.86-1.962.10.216768721.13889.7
1.96-2.082.10.136782721.15591.1
2.08-2.242.10.091799361.1693.2
2.24-2.462.20.069825261.09396.1
2.46-2.822.30.053836941.0497.6
2.82-3.552.40.037840131.01197.8
3.55-502.40.026833551.05197.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q08

2q08


Resolution: 1.65→19.99 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.069 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 37962 5 %RANDOM
Rwork0.187 ---
obs0.189 759011 89.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.888 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41373 0 32 4909 46314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02242427
X-RAY DIFFRACTIONr_angle_refined_deg1.6041.9457549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.40255065
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47623.9192225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.342157530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9115343
X-RAY DIFFRACTIONr_chiral_restr0.1160.26181
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0232593
X-RAY DIFFRACTIONr_nbd_refined0.2140.222479
X-RAY DIFFRACTIONr_nbtor_refined0.3110.229215
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.24624
X-RAY DIFFRACTIONr_metal_ion_refined0.1870.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.264
X-RAY DIFFRACTIONr_mcbond_it1.4561.525853
X-RAY DIFFRACTIONr_mcangle_it3.7342040751
X-RAY DIFFRACTIONr_scbond_it6.8612019103
X-RAY DIFFRACTIONr_scangle_it4.4164.516757
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 1647 -
Rwork0.287 30914 -
obs-32561 52.26 %

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