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- PDB-2q08: Crystal structure of the protein BH0493 from Bacillus halodurans ... -

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Basic information

Entry
Database: PDB / ID: 2q08
TitleCrystal structure of the protein BH0493 from Bacillus halodurans C-125 complexed with ZN
ComponentsBH0493 protein
KeywordsISOMERASE / Structural Genomics / NYSGXRC / target 9247a / Glucoronate isomerase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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 / SAD / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Raushel, F. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Glucoronate Isomerase from Bacillus halodurans.
Authors: Fedorov, A.A. / Fedorov, E.V. / Patskovsky, Y. / Sauder, J.M. / Burley, S.K. / Raushel, F.M. / Almo, S.C.
History
DepositionMay 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 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: 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)601,12928
Polymers600,08212
Non-polymers1,04716
Water17,348963
1
A: BH0493 protein
B: BH0493 protein
C: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2827
Polymers150,0213
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12220 Å2
ΔGint-176 kcal/mol
Surface area41330 Å2
MethodPISA
2
D: BH0493 protein
E: BH0493 protein
F: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2827
Polymers150,0213
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint-176 kcal/mol
Surface area41330 Å2
MethodPISA
3
G: BH0493 protein
H: BH0493 protein
I: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2827
Polymers150,0213
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-177 kcal/mol
Surface area41280 Å2
MethodPISA
4
J: BH0493 protein
K: BH0493 protein
L: BH0493 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,2827
Polymers150,0213
Non-polymers2624
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12200 Å2
ΔGint-176 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.274, 120.967, 126.241
Angle α, β, γ (deg.)78.82, 78.67, 80.42
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the trimer ABC, or DEF, or GHI or JKL.

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Components

#1: Protein
BH0493 protein


Mass: 50006.852 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KFI6
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 963 / 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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 45% Polypropylene glycol P400, 0.1M Bis-tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 2, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 415887 / Num. obs: 415887 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.088

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→24.93 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 261226.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 20660 5 %RANDOM
Rwork0.226 ---
all0.226 415887 --
obs0.226 415887 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.5021 Å2 / ksol: 0.36164 e/Å3
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å2-3.01 Å2-3.55 Å2
2---1.61 Å2-3.78 Å2
3---3.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40812 0 16 963 41791
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.732
X-RAY DIFFRACTIONc_scbond_it1.812
X-RAY DIFFRACTIONc_scangle_it2.632.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.342 1486 4.9 %
Rwork0.318 28875 -
obs--65.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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