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- PDB-1z2i: CRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENA... -

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Basic information

Entry
Database: PDB / ID: 1z2i
TitleCRYSTAL STRUCTURE OF Agrobacterium tumefaciens MALATE DEHYDROGENASE, NEW YORK STRUCTURAL GENOMICS CONSORTIUM
Componentsmalate dehydrogenase
KeywordsOXIDOREDUCTASE / MALATE DEHYDROGENASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...Hypothetical oxidoreductase yiak; domain 3 / Malate/L-lactate dehydrogenase-like / Malate/L-sulfolactate/L-lactate dehydrogenase-like superfamily / Malate/L-sulfolactate/L-lactate dehydrogenase-like, NADPH binding domain / Malate/L-sulfolactate/L-lactate dehydrogenase-like, alpha-helical domain / Malate/L-lactate dehydrogenase / Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 / Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel / Malate/L-lactate/L-sulpholactate dehydrogenase, NADPH binding domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.2 Å
AuthorsPatskovsky, Y. / Almo, S.C. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Agrobacterium Tumefaciens Malate Dehydrogenase
Authors: Patskovsky, Y. / Almo, S.C.
History
DepositionMar 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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

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Assembly

Deposited unit
A: malate dehydrogenase
B: malate dehydrogenase
C: malate dehydrogenase
D: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,8478
Polymers153,1934
Non-polymers2,6544
Water12,592699
1
A: malate dehydrogenase
B: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9244
Polymers76,5972
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-74 kcal/mol
Surface area24970 Å2
MethodPISA
2
C: malate dehydrogenase
D: malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9244
Polymers76,5972
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-75 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.220, 98.220, 146.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
DetailsThe biological assembly is a homodimer. The asymmetric unit contains two homodimers, AB and CD chains respectively

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Components

#1: Protein
malate dehydrogenase


Mass: 38298.363 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: AGR_L_3209 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7CRW4
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG3350, 0.1M Bis-Tris, 0.1M Lithium sulfate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 87 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 11, 2005 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 71329 / Num. obs: 71329 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.9 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.083 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4270 / Rsym value: 0.255 / % possible all: 53.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 152570.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2164 3 %RANDOM
Rwork0.239 ---
all0.246 71329 --
obs0.239 71004 88.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.7732 Å2 / ksol: 0.313226 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.02 Å2-0.2 Å20 Å2
2---3.02 Å20 Å2
3---6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 176 699 11399
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it3.783.5
X-RAY DIFFRACTIONc_mcangle_it5.265
X-RAY DIFFRACTIONc_scbond_it6.16
X-RAY DIFFRACTIONc_scangle_it7.947.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 226 2.9 %
Rwork0.31 7482 -
obs-7482 57.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD.PARAMNAD.TOP

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