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- PDB-1ib6: CRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1ib6
TitleCRYSTAL STRUCTURE OF R153C E. COLI MALATE DEHYDROGENASE
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / MALATE DEHYDROGENASE / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity ...malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity / protein homodimerization activity / membrane / cytoplasm / cytosol
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBell, J.K. / Yennawar, H.P. / Wright, S.K. / Thompson, J.R. / Viola, R.E. / Banaszak, L.J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: Structural Analyses of a Malate Dehydrogenase with a Variable Active Site
Authors: Bell, J.K. / Yennawar, H.P. / Wright, S.K. / Thompson, J.R. / Viola, R.E. / Banaszak, L.J.
#1: Journal: To be Published
Title: ALTERATION OF THE SPECIFICITY OF MALATE DEHYDROGENASE BY CHEMICAL MODIFICATION OF AN ACTIVE SITE ARGININE
Authors: Kirk, S.K. / Viola, R.E.
History
DepositionMar 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)131,81913
Polymers129,2534
Non-polymers2,5679
Water5,008278
1
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4825
Polymers64,6262
Non-polymers8563
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-71 kcal/mol
Surface area22990 Å2
MethodPISA
2
C: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3378
Polymers64,6262
Non-polymers1,7116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-116 kcal/mol
Surface area22580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.140, 53.080, 164.290
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MALATE DEHYDROGENASE


Mass: 32313.141 Da / Num. of mol.: 4 / Mutation: R153C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MDH / Plasmid: PEM6 / Production host: Escherichia coli (E. coli) / References: UniProt: P61889, malate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.49 Å3/Da / Density % sol: 50.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: TRIS-MALEATE, PEG 3350, AMMONIUM SULFATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-maleate1reservoir
224-30 %PEG33501reservoir
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 1999 / Details: OSMIC
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. all: 201844 / Num. obs: 73723 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.368 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 201844
Reflection shell
*PLUS
% possible obs: 84.8 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.5refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3790211.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.244 7418 10.1 %RANDOM
Rwork0.192 ---
all0.192 201844 --
obs0.192 73723 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.07 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9068 0 162 278 9508
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.25 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4142 1367 11 %
Rwork0.402 12466 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAD_XPLOR_PAR.TXTNAD_XPLOR_TOP.TXT
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 47.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.22
LS refinement shell
*PLUS
% reflection Rfree: 11 % / Rfactor Rwork: 0.402

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