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- PDB-3gvi: Crystal structure of Lactate/malate dehydrogenase from Brucella m... -

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Basic information

Entry
Database: PDB / ID: 3gvi
TitleCrystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / LACTATE/MALATE DEHYDROGENASE / BRUCELLA MELITENSIS / NAD / Tricarboxylic acid cycle / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain ...Malate dehydrogenase, type 3 / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Malate dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Lactate/malate dehydrogenase from Brucella melitensis in complex with ADP
Authors: Abendroth, J. / Staker, B.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,78712
Polymers204,2236
Non-polymers2,5636
Water23,6181311
1
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8588
Polymers136,1494
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17510 Å2
ΔGint-84 kcal/mol
Surface area40950 Å2
MethodPISA
2
E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules

E: Malate dehydrogenase
F: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8588
Polymers136,1494
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area17380 Å2
ΔGint-86 kcal/mol
Surface area40740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.390, 193.900, 102.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 320
2114B1 - 320
3114C1 - 320
4114D1 - 320
5114E1 - 320
6114F1 - 320

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Components

#1: Protein
Malate dehydrogenase /


Mass: 34037.238 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Gene: mdh, BAB1_1927 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YLR9, malate dehydrogenase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1311 / 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: 53.01 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ SCREEN, H3: 25% PEG 3350, 100MM BISTRIS, BRABA.00005.A AT 28.5MG/ML, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97933
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.25→193.9 Å / Num. all: 102350 / Num. obs: 99622 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 28.89 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.82
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 2 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 5.6 / Num. unique all: 7486 / % possible all: 83.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 3GVH
Resolution: 2.25→193 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.079 / SU ML: 0.128 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5000 5 %RANDOM
Rwork0.174 ---
obs0.177 99617 97.3 %-
all-99617 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å2-0 Å2
2--0.67 Å2-0 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.25→193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13710 0 162 1311 15183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214106
X-RAY DIFFRACTIONr_bond_other_d0.0020.029138
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.99319173
X-RAY DIFFRACTIONr_angle_other_deg0.927322518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5851871
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.25425.171497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.105152251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4131548
X-RAY DIFFRACTIONr_chiral_restr0.0860.22255
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022639
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7561.59271
X-RAY DIFFRACTIONr_mcbond_other0.2321.53892
X-RAY DIFFRACTIONr_mcangle_it1.412214748
X-RAY DIFFRACTIONr_scbond_it2.3434835
X-RAY DIFFRACTIONr_scangle_it3.7484.54425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3760 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.270.5
Bmedium positional0.270.5
Cmedium positional0.260.5
Dmedium positional0.360.5
Emedium positional0.270.5
Fmedium positional0.410.5
Amedium thermal0.982
Bmedium thermal0.782
Cmedium thermal0.692
Dmedium thermal0.852
Emedium thermal0.832
Fmedium thermal1.212
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 305 -
Rwork0.286 5960 -
obs--83.7 %

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