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- PDB-4hn8: Crystal structure of a putative D-glucarate dehydratase from Pseu... -

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Basic information

Entry
Database: PDB / ID: 4hn8
TitleCrystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp
ComponentsD-glucarate dehydratase
KeywordsLYASE / structural genomics / PSI-Biology / Protein Structure Initiative / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


glucarate dehydratase activity / glucarate dehydratase
Similarity search - Function
D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / 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 ...D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / 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-glucarate dehydratase
Similarity search - Component
Biological speciesPseudomonas mendocina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be published
Title: Crystal structure of a putative D-glucarate dehydratase from Pseudomonas mendocina ymp
Authors: Hegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A.
History
DepositionOct 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Structure summary
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-glucarate dehydratase
B: D-glucarate dehydratase
C: D-glucarate dehydratase
D: D-glucarate dehydratase
E: D-glucarate dehydratase
F: D-glucarate dehydratase
G: D-glucarate dehydratase
H: D-glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,90617
Polymers423,0778
Non-polymers8299
Water9,764542
1
A: D-glucarate dehydratase
B: D-glucarate dehydratase
C: D-glucarate dehydratase
D: D-glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,9999
Polymers211,5394
Non-polymers4605
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-5 kcal/mol
Surface area57680 Å2
MethodPISA
2
E: D-glucarate dehydratase
F: D-glucarate dehydratase
G: D-glucarate dehydratase
H: D-glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,9078
Polymers211,5394
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-8 kcal/mol
Surface area57620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.355, 148.835, 198.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
D-glucarate dehydratase


Mass: 52884.645 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas mendocina (bacteria) / Strain: ymp / Gene: Pmen_1214 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4XRL3, glucarate dehydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium pH 7.5, 10% v/v Propanol, 20% PEG 4000, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 189005 / Num. obs: 189005 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.174 / Rsym value: 0.11 / Χ2: 1.132 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
2.2-2.249.90.8742.5193710.7350.979100
2.24-2.28100.80293530.983100
2.28-2.32100.72293541.004100
2.32-2.3710.10.64793310.985100
2.37-2.4210.10.57294101.013100
2.42-2.4810.10.51194010.97100
2.48-2.5410.20.44793320.998100
2.54-2.6110.20.40794150.985100
2.61-2.6910.20.35793741.003100
2.69-2.7710.20.32593851.014100
2.77-2.8710.30.26994491.04100
2.87-2.9910.30.22993771.074100
2.99-3.1210.30.18793991.114100
3.12-3.2910.30.15394471.109100
3.29-3.4910.30.12494691.148100
3.49-3.7610.30.10395061.219100
3.76-4.1410.20.08994961.26100
4.14-4.7410.10.07895491.328100
4.74-5.979.80.08196211.55100
5.97-509.80.0799661.84199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EC7

1ec7


Resolution: 2.2→46.18 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.1557 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8519 / SU B: 5.284 / SU ML: 0.133 / SU R Cruickshank DPI: 0.2441 / SU Rfree: 0.1937 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 9478 5 %RANDOM
Rwork0.1756 ---
obs0.1779 188753 99.73 %-
all-188753 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.89 Å2 / Biso mean: 25.905 Å2 / Biso min: 7.42 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26359 0 54 542 26955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01927227
X-RAY DIFFRACTIONr_bond_other_d00.0226121
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.96936923
X-RAY DIFFRACTIONr_angle_other_deg0.646359750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62653456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55622.8011303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.874154116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.94615297
X-RAY DIFFRACTIONr_chiral_restr0.0750.23959
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02131426
X-RAY DIFFRACTIONr_gen_planes_other00.026531
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 700 -
Rwork0.237 12804 -
all-13504 -
obs--97.49 %

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