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- PDB-3bsm: Crystal structure of D-mannonate dehydratase from Chromohalobacte... -

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Basic information

Entry
Database: PDB / ID: 3bsm
TitleCrystal structure of D-mannonate dehydratase from Chromohalobacter salexigens
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsLYASE / structural genomics / NYSGXRC / target 9262h / clone 9262h1BCt8p1 / D-MANNONATE DEHYDRATASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-galactonate dehydratase family member ManD
Similarity search - Component
Biological speciesChromohalobacter salexigens DSM 3043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Toro, R. / 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 D-mannonate dehydratase from Chromohalobacter salexigens.
Authors: Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme


Theoretical massNumber of molelcules
Total (without water)185,9334
Polymers185,9334
Non-polymers00
Water3,819212
1
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme


Theoretical massNumber of molelcules
Total (without water)92,9672
Polymers92,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
MethodPISA
2
C: Mandelate racemase/muconate lactonizing enzyme

D: Mandelate racemase/muconate lactonizing enzyme


Theoretical massNumber of molelcules
Total (without water)92,9672
Polymers92,9672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2420 Å2
MethodPISA
3
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme


Theoretical massNumber of molelcules
Total (without water)371,8668
Polymers371,8668
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area34600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.125, 163.070, 84.553
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 46483.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens DSM 3043 (bacteria)
Species: Chromohalobacter salexigens / Strain: DSM 3043 / NCIMB 13768 / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 39.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 0.1M MES, 0.2M Ammonium sulfate, 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: Feb 25, 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: 2.2→25 Å / Num. all: 77523 / Num. obs: 77523 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.078

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→24.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1925641.62 / 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
Rfree0.268 3849 5 %RANDOM
Rwork0.243 ---
all0.243 77523 --
obs0.243 77523 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.3762 Å2 / ksol: 0.392954 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.92 Å20 Å20 Å2
2--16.95 Å20 Å2
3----14.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11300 0 0 212 11512
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.361 351 4.7 %
Rwork0.326 7138 -
obs--97.5 %
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 DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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