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- PDB-4h7p: Crystal structure of a putative Cytosolic malate dehydrogenase fr... -

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Basic information

Entry
Database: PDB / ID: 4h7p
TitleCrystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Leishmania major / Malate dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / malate metabolic process / oxaloacetate metabolic process / NADH metabolic process / tricarboxylic acid cycle / nucleotide binding / cytosol
Similarity search - Function
Malate dehydrogenase, type 2 / 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 ...Malate dehydrogenase, type 2 / 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
Malate dehydrogenase
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a putative Cytosolic malate dehydrogenase from Leishmania major Friedlin
Authors: Abendroth, J. / Sankaran, B. / Staker, B.L. / Stewart, L.J. / Myler, P. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4467
Polymers72,9652
Non-polymers4805
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.580, 65.660, 77.650
Angle α, β, γ (deg.)90.000, 110.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malate dehydrogenase /


Mass: 36482.691 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: cMDH, LMJF_28_2860 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4Q7X6, malate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: EmeraldBio JCSG+ screen h7: 25% PEG 3350, 200mM ammonium sulphate, 100mM BisTris pH 5.5; LemaA.01212.a.A1.P001468 at 20mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2012
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 146529 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 21.987 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 24.71
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.3-1.330.3364.114802010351194
1.33-1.370.2835.355866810432196.6
1.37-1.410.2216.685883610137197.1
1.41-1.450.1947.87595309837197.3
1.45-1.50.23710.731026249643197.4
1.5-1.550.19612.871072879266197.8
1.55-1.610.15315.621054189074197.9
1.61-1.680.12318.281005558648198.3
1.68-1.750.10121.24971808384198.5
1.75-1.840.08425.16927058000198.5
1.84-1.940.06930.6883507641199
1.94-2.060.05836.04834697271199.2
2.06-2.20.05142.33779206823199.3
2.2-2.370.04646.78718556369199.3
2.37-2.60.04450.66655175893199.6
2.6-2.910.04454.28587705355199.9
2.91-3.360.04257.65508844720199.8
3.36-4.110.03660.52428734018199.7
4.11-5.810.03162.74321133100199.1
5.81-500.02959.37142191567188.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.53 Å
Translation3.5 Å19.53 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IZ9
Resolution: 1.3→28.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.1803 / WRfactor Rwork: 0.1554 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.901 / SU B: 1.236 / SU ML: 0.026 / SU R Cruickshank DPI: 0.0424 / SU Rfree: 0.0459 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1785 7367 5 %RANDOM
Rwork0.1522 ---
all0.1534 149715 --
obs0.1534 146506 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.48 Å2 / Biso mean: 21.4934 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20.57 Å2
2---0.1 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.3→28.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 25 635 5098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194629
X-RAY DIFFRACTIONr_bond_other_d0.0010.024512
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.9736345
X-RAY DIFFRACTIONr_angle_other_deg0.847310322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58123.269156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21715695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2041532
X-RAY DIFFRACTIONr_chiral_restr0.1020.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215321
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 533 -
Rwork0.221 9815 -
all-10348 -
obs--93.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.45030.1748-0.37840.3019-0.03630.9175-0.02020.07420.0242-0.02060.01940.00840.0346-0.07370.00080.00810.0006-0.00440.0159-0.00140.0374-4.60320.06362.79
20.4802-0.0082-0.09960.27250.00211.0520.0202-0.06930.01950.058-0.00720.0280.0339-0.0025-0.0130.0221-0.01280.00960.0206-0.01390.0268-13.2216.47895.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 324
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B2 - 324
4X-RAY DIFFRACTION2B400 - 402

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