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- PDB-1d3a: CRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENAS... -

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Basic information

Entry
Database: PDB / ID: 1d3a
TitleCRYSTAL STRUCTURE OF THE WILD TYPE HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
ComponentsHALOPHILIC MALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD AND 3 SORTS OF COMPLEX SALT BRIDGES
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate metabolic process / pyruvate metabolic process / tricarboxylic acid cycle / cytoplasm
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 ...: / 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
Malate dehydrogenase
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.94 Å
AuthorsRichard, S.B. / Madern, D. / Garcin, E. / Zaccai, G.
Citation
Journal: Biochemistry / Year: 2000
Title: Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui.
Authors: Richard, S.B. / Madern, D. / Garcin, E. / Zaccai, G.
#1: Journal: ARCHAEA : A LABORATORY MANUAL. V.[1]. HALOPHILES / Year: 1995
Title: Protocol 21: the MPD-NACL-H2O System for the Crystallization of Halophilic Proteins
Authors: Richard, S.B. / Bonnete, F. / Dym, O. / Zaccai, G.
#2: Journal: Science / Year: 1995
Title: Structural Features Stabilizing Halophilic Malate Dehydrogenase from an Archaebacterium
Authors: Dym, O. / Mevarech, M. / Sussman, J.L.
#3: Journal: Eur.J.Biochem. / Year: 1995
Title: Mutation at a Single Amino Acid Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula Marismortui in physiological salts
Authors: Madern, D. / Pfister, C. / Zaccai, G.
#4: Journal: Biochemistry / Year: 1993
Title: Cloning, Sequencing, and Expression in Escherichia Coli of the Gene Coding for Malate Dehydrogenase of the Extremely Halophilic Archaebacterium Haloarcula Marismortui
Authors: Cendrin, F. / Chroboczek, J. / Zaccai, G. / Eisenberg, H. / Mevarech, M.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 9, 2014Group: Database references
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Downloads & links

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Assembly

Deposited unit
A: HALOPHILIC MALATE DEHYDROGENASE
B: HALOPHILIC MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5075
Polymers65,4132
Non-polymers943
Water57632
1
A: HALOPHILIC MALATE DEHYDROGENASE
B: HALOPHILIC MALATE DEHYDROGENASE
hetero molecules

A: HALOPHILIC MALATE DEHYDROGENASE
B: HALOPHILIC MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,01410
Polymers130,8264
Non-polymers1886
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area12500 Å2
ΔGint-64 kcal/mol
Surface area43510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.780, 131.330, 125.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HALOPHILIC MALATE DEHYDROGENASE


Mass: 32706.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: MPD-NaCl-H2O system, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 70 %
Crystal grow
*PLUS
Temperature: 6 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
21.8 M1dropNaCl
358 %MPD1drop
44.3 mM1dropCsCl
514 mg/mlprotein1drop
660-70 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 284 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 22, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. obs: 99423 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 82.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.2
Reflection shellResolution: 2.94→3.07 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.332 / Num. unique all: 19960 / % possible all: 94.9
Reflection
*PLUS
Num. obs: 19960 / Num. measured all: 99423
Reflection shell
*PLUS
% possible obs: 94.5 % / Num. unique obs: 3237

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
XDSdata scaling
RefinementResolution: 2.94→30 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 2600643.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: using maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1003 4.9 %RANDOM
Rwork0.202 ---
all-20664 --
obs-20523 99.2 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.17 Å20 Å20 Å2
2--17.61 Å20 Å2
3----14.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4602 0 3 32 4637
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it5.741.5
X-RAY DIFFRACTIONc_mcangle_it8.182
X-RAY DIFFRACTIONc_scbond_it8.032
X-RAY DIFFRACTIONc_scangle_it10.722.5
LS refinement shellResolution: 2.94→3.04 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 169 5 %
Rwork0.311 3222 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARA.INP
X-RAY DIFFRACTION3CIS_PEPTIDE_DIM.PARAM
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.188 / Num. reflection obs: 15920
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 61.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.024
X-RAY DIFFRACTIONc_angle_deg2.09
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.34
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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