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- PDB-3nxl: Crystal structure of Glucarate dehydratase from Burkholderia cepa... -

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Basic information

Entry
Database: PDB / ID: 3nxl
TitleCrystal structure of Glucarate dehydratase from Burkholderia cepacia complexed with magnesium
ComponentsGlucarate dehydratase
KeywordsLYASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


glucarate dehydratase activity / glucarate dehydratase / metal ion binding
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
CARBONATE ION / D-glucarate dehydratase
Similarity search - Component
Biological speciesBurkholderia sp. 383 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.885 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Gerlt, J.A. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Glucarate dehydratase from Burkholderia cepacia complexed with magnesium
Authors: Fedorov, A.A. / Fedorov, E.V. / Gerlt, J.A. / Burley, S.K. / Almo, S.C.
History
DepositionJul 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 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_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.pdbx_leaving_atom_flag / _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_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

Downloads & links

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Assembly

Deposited unit
A: Glucarate dehydratase
B: Glucarate dehydratase
C: Glucarate dehydratase
D: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,18412
Polymers208,8474
Non-polymers3378
Water15,853880
1
A: Glucarate dehydratase
C: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5926
Polymers104,4232
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucarate dehydratase
D: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5926
Polymers104,4232
Non-polymers1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2963
Polymers52,2121
Non-polymers842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2963
Polymers52,2121
Non-polymers842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2963
Polymers52,2121
Non-polymers842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2963
Polymers52,2121
Non-polymers842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)165.289, 121.452, 108.652
Angle α, β, γ (deg.)90.00, 92.60, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer

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Components

#1: Protein
Glucarate dehydratase


Mass: 52211.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. 383 (bacteria) / Gene: Bcep18194_A3396 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39KL8, glucarate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 880 / 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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3350,0.2M sodium malonate, 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: Apr 29, 2010
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: 1.885→34.235 Å / Num. all: 167926 / Num. obs: 167926 / % possible obs: 97.52 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.885→34.235 Å / SU ML: 0.22 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 8434 5.02 %RANDOM
Rwork0.1901 ---
all0.1917 167926 --
obs0.1917 167926 97.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.642 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.9297 Å2-0 Å2-6.9204 Å2
2---5.8049 Å2-0 Å2
3----2.1249 Å2
Refinement stepCycle: LAST / Resolution: 1.885→34.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12942 0 20 880 13842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713338
X-RAY DIFFRACTIONf_angle_d0.98418156
X-RAY DIFFRACTIONf_dihedral_angle_d18.0234777
X-RAY DIFFRACTIONf_chiral_restr0.0661983
X-RAY DIFFRACTIONf_plane_restr0.0042423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8854-1.90690.3161600.32412973X-RAY DIFFRACTION54
1.9069-1.92930.33282460.30394749X-RAY DIFFRACTION87
1.9293-1.95280.33542420.28515015X-RAY DIFFRACTION93
1.9528-1.97750.28882740.27185367X-RAY DIFFRACTION98
1.9775-2.00360.30172890.25275368X-RAY DIFFRACTION99
2.0036-2.0310.3022550.24795423X-RAY DIFFRACTION99
2.031-2.060.30633070.245446X-RAY DIFFRACTION100
2.06-2.09080.26172870.23625430X-RAY DIFFRACTION100
2.0908-2.12340.27942720.22845370X-RAY DIFFRACTION100
2.1234-2.15820.25733040.22395381X-RAY DIFFRACTION100
2.1582-2.19540.27632700.21215429X-RAY DIFFRACTION100
2.1954-2.23540.24942710.20855457X-RAY DIFFRACTION100
2.2354-2.27830.25272980.20355416X-RAY DIFFRACTION100
2.2783-2.32480.24572850.20365412X-RAY DIFFRACTION100
2.3248-2.37540.23073020.19755414X-RAY DIFFRACTION100
2.3754-2.43060.25592960.19655421X-RAY DIFFRACTION100
2.4306-2.49140.22772920.19955396X-RAY DIFFRACTION100
2.4914-2.55870.25773170.18945407X-RAY DIFFRACTION100
2.5587-2.6340.20612720.18835494X-RAY DIFFRACTION100
2.634-2.7190.25452990.19875420X-RAY DIFFRACTION100
2.719-2.81610.253060.19745395X-RAY DIFFRACTION100
2.8161-2.92880.22533220.19255464X-RAY DIFFRACTION100
2.9288-3.0620.20962890.19515403X-RAY DIFFRACTION100
3.062-3.22330.22293000.18945444X-RAY DIFFRACTION100
3.2233-3.42510.20242630.17785487X-RAY DIFFRACTION100
3.4251-3.68930.18572840.16835483X-RAY DIFFRACTION100
3.6893-4.060.18332690.15445467X-RAY DIFFRACTION100
4.06-4.64630.1662940.14695486X-RAY DIFFRACTION100
4.6463-5.84910.18122750.15755514X-RAY DIFFRACTION100
5.8491-34.24040.17542940.17095561X-RAY DIFFRACTION100

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