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- PDB-3hk9: Crystal structure of uronate isomerase from Bacillus halodurans c... -

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Basic information

Entry
Database: PDB / ID: 3hk9
TitleCrystal structure of uronate isomerase from Bacillus halodurans complexed with zinc and D-Glucuronate
ComponentsUronate isomerase
KeywordsISOMERASE / uronate isomerase / D-Glucuronate / Mechanism of the reaction
Function / homologyuronate isomerase, domain 2, chain A / uronate isomerase, domain 2, chain A / Metal-dependent hydrolase / Orthogonal Bundle / Mainly Alpha / metal ion binding / CARBONATE ION / D-glucuronic acid / BH0493 protein
Function and homology information
Biological speciesBacillus halodurans C-125 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Nguyen, T.T. / Raushel, F.M. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2009
Title: The mechanism of the reaction catalyzed by uronate isomerase illustrates how an isomerase may have evolved from a hydrolase within the amidohydrolase superfamily.
Authors: Nguyen, T.T. / Fedorov, A.A. / Williams, L. / Fedorov, E.V. / Li, Y. / Xu, C. / Almo, S.C. / Raushel, F.M.
History
DepositionMay 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Atomic model
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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

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Assembly

Deposited unit
A: Uronate isomerase
B: Uronate isomerase
C: Uronate isomerase
D: Uronate isomerase
E: Uronate isomerase
F: Uronate isomerase
G: Uronate isomerase
H: Uronate isomerase
I: Uronate isomerase
J: Uronate isomerase
K: Uronate isomerase
L: Uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)604,05952
Polymers600,08212
Non-polymers3,97640
Water32,8591824
1
A: Uronate isomerase
B: Uronate isomerase
C: Uronate isomerase
D: Uronate isomerase
E: Uronate isomerase
H: Uronate isomerase
K: Uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,39131
Polymers350,0487
Non-polymers2,34324
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-25.8 kcal/mol
Surface area41370 Å2
MethodPISA
2
A: Uronate isomerase
B: Uronate isomerase
D: Uronate isomerase
E: Uronate isomerase
F: Uronate isomerase
I: Uronate isomerase
L: Uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,35630
Polymers350,0487
Non-polymers2,30823
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11350 Å2
ΔGint-26.8 kcal/mol
Surface area41290 Å2
MethodPISA
3
B: Uronate isomerase
C: Uronate isomerase
F: Uronate isomerase
G: Uronate isomerase
H: Uronate isomerase
I: Uronate isomerase
J: Uronate isomerase
L: Uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,62233
Polymers400,0558
Non-polymers2,56725
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-22.5 kcal/mol
Surface area41420 Å2
MethodPISA
4
C: Uronate isomerase
D: Uronate isomerase
G: Uronate isomerase
H: Uronate isomerase
J: Uronate isomerase
K: Uronate isomerase
L: Uronate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,41631
Polymers350,0487
Non-polymers2,36824
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-25.2 kcal/mol
Surface area41450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.091, 156.880, 185.206
Angle α, β, γ (deg.)90.00, 115.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 24 molecules ABCDEFGHIJKL

#1: Protein
Uronate isomerase / 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) / Strain: C-125 / DSM 18197 / FERM 7344 / JCM 9153 / Gene: BH0493 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KFI6
#2: Sugar
ChemComp-REL / D-glucuronic acid / D-Glucuronate / alpha-D-glucofuranuronic acid / Glucuronic acid


Type: D-saccharide / Mass: 194.139 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C6H10O7

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Non-polymers , 4 types, 1852 molecules

#3: Chemical
ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1824 / 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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350, 0.2M Ammonium citrate, pH 7.0, 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 / Details: mirrors
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: 2.1→25 Å / Num. all: 404122 / Num. obs: 404122 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.074

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Q08

2q08


Resolution: 2.1→24.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1778514.91 / 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
Rfree0.258 20316 5 %RANDOM
Rwork0.227 ---
all0.229 404122 --
obs0.229 404122 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.3742 Å2 / ksol: 0.361085 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.16 Å2
2--2.78 Å20 Å2
3----3.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40848 0 220 1824 42892
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_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.72
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.1→2.18 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.318 1882 5 %
Rwork0.296 35495 -
obs-35495 91.5 %
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 DIFFRACTION4INH_par.txtINH_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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