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- PDB-2dw7: Crystal structure of D-tartrate dehydratase from Bradyrhizobium j... -

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Basic information

Entry
Database: PDB / ID: 2dw7
TitleCrystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate
ComponentsBll6730 protein
KeywordsLYASE / D-tartrate dehydratase / Enolase superfamily / meso-tartrate
Function / homology
Function and homology information


D(-)-tartrate dehydratase / D(-)-tartrate dehydratase activity / D-galactonate catabolic process / hydro-lyase activity / protein homooligomerization / magnesium ion binding
Similarity search - Function
D-tartrate dehydratase / 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-tartrate dehydratase / 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
S,R MESO-TARTARIC ACID / D(-)-tartrate dehydratase
Similarity search - Component
Biological speciesBradyrhizobium japonicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Yew, W.S. / Wood, B.M. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Biochemistry / Year: 2006
Title: Evolution of Enzymatic Activities in the Enolase Superfamily: d-Tartrate Dehydratase from Bradyrhizobium japonicum
Authors: Yew, W.S. / Fedorov, A.A. / Fedorov, E.V. / Wood, B.M. / Almo, S.C. / Gerlt, J.A.
History
DepositionAug 7, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bll6730 protein
B: Bll6730 protein
C: Bll6730 protein
D: Bll6730 protein
E: Bll6730 protein
F: Bll6730 protein
G: Bll6730 protein
H: Bll6730 protein
I: Bll6730 protein
J: Bll6730 protein
K: Bll6730 protein
L: Bll6730 protein
M: Bll6730 protein
N: Bll6730 protein
O: Bll6730 protein
P: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)692,56848
Polymers689,77816
Non-polymers2,79032
Water8,089449
1
A: Bll6730 protein
B: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-28 kcal/mol
Surface area26780 Å2
MethodPISA
2
C: Bll6730 protein
D: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area26770 Å2
MethodPISA
3
E: Bll6730 protein
F: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-26 kcal/mol
Surface area26630 Å2
MethodPISA
4
G: Bll6730 protein
H: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area26690 Å2
MethodPISA
5
I: Bll6730 protein
J: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-26 kcal/mol
Surface area26720 Å2
MethodPISA
6
K: Bll6730 protein
L: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-27 kcal/mol
Surface area26740 Å2
MethodPISA
7
M: Bll6730 protein
N: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-27 kcal/mol
Surface area26560 Å2
MethodPISA
8
O: Bll6730 protein
P: Bll6730 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5716
Polymers86,2222
Non-polymers3494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-19 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.837, 162.542, 168.181
Angle α, β, γ (deg.)117.76, 90.03, 90.67
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is the dimer. There are 8 dimers in the asymmetric unit.

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Components

#1: Protein
Bll6730 protein / D-tartrate Dehydratase


Mass: 43111.109 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium japonicum (bacteria) / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q89FH0, D(-)-tartrate dehydratase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 16% PEG 3350, 0.1M Bis.Tris, 5% acetone, pH 5.5, 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: 0.97911 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 12, 2006
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 223601 / Num. obs: 223601 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.59 Å / % possible all: 78.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
EPMRphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TZZ

1tzz


Resolution: 2.5→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.265 11133 RANDOM
Rwork0.241 --
all0.243 223601 -
obs0.243 223601 -
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48352 0 176 449 48977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.33

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