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- PDB-2hlp: CRYSTAL STRUCTURE OF THE E267R MUTANT OF A HALOPHILIC MALATE DEHY... -

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Basic information

Entry
Database: PDB / ID: 2hlp
TitleCRYSTAL STRUCTURE OF THE E267R MUTANT OF A HALOPHILIC MALATE DEHYDROGENASE IN THE APO FORM
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / HALOPHILIC / ION-BINDING / SALT BRIDGES / MALATE DEHYDROGENASE
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase activity / carboxylic acid 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 / 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
Malate dehydrogenase
Similarity search - Component
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.59 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: AMYLOID / 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: A Single Amino Acid Mutation Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula marismortui
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
DepositionApr 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)65,5635
Polymers65,4692
Non-polymers943
Water4,360242
1
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,12610
Polymers130,9384
Non-polymers1886
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Unit cell
Length a, b, c (Å)114.160, 129.980, 123.450
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 MALATE DEHYDROGENASE /


Mass: 32734.613 Da / Num. of mol.: 2 / Mutation: E267R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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 / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHREE KINDS OF COMPLEX SALT BRIDGES MAY BE DESCRIBED INCLUDING: CL, LYS A 205, ASP D 211, ARG D ...THREE KINDS OF COMPLEX SALT BRIDGES MAY BE DESCRIBED INCLUDING: CL, LYS A 205, ASP D 211, ARG D 207, GLU A 188, GLU D 188, ARG A 207, ASP A 211, LYS D 203, CL, AND ITS SYMMETRY RELATED; ASP A 209, ARG D 292, GLU D 299 AND ITS 3 OTHERS SYMMETRY RELATED; LYS A 243, GLU A 247, NA+, GLU B 247, LYS B 243, AND ITS SYMMETRY RELATED.

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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: 3.49 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.6 / Details: 1.7M NACL, 20MM TRIS, PH 7.6, 57% MPD
Crystal grow
*PLUS
Temperature: 6 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
250 mMTris-HCl1drop
31.8 M1dropNaCl
458 %MPD1drop
560-70 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 279 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2.59→28 Å / Num. obs: 26445 / % possible obs: 88.7 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.3
Reflection shellResolution: 2.59→2.75 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.2 / % possible all: 69.7
Reflection
*PLUS
% possible obs: 88.5 % / Num. measured all: 159628 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 71.3 %

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Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
CCP4data scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1HLP

1hlp


Resolution: 2.59→28 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1221 4.8 %RANDOM
Rwork0.194 ---
obs-25280 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.87 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso mean: 41.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2--3.33 Å20 Å2
3----3.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.59→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 3 242 4851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.59→2.75 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 144 4.5 %
Rwork0.309 3031 -
obs--67 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.232 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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