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- PDB-1ur5: Stabilization of a Tetrameric Malate Dehydrogenase by Introductio... -

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Basic information

Entry
Database: PDB / ID: 1ur5
TitleStabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer/Dimer Interface
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / TRICARBOXYLIC ACID CYCLE / 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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesCHLOROFLEXUS AURANTIACUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBjork, A. / Dalhus, B. / Mantzilas, D. / Eijsink, V.G.H. / Sirevag, R.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Stabilization of a Tetrameric Malate Dehydrogenase by Introduction of a Disulfide Bridge at the Dimer-Dimer Interface
Authors: Bjork, A. / Dalhus, B. / Mantzilas, D. / Eijsink, V.G.H. / Sirevag, R.
History
DepositionOct 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALATE DEHYDROGENASE
C: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,58213
Polymers65,5002
Non-polymers2,08311
Water9,854547
1
A: MALATE DEHYDROGENASE
C: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
C: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,16526
Polymers130,9994
Non-polymers4,16522
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+4/31
MethodPQS
Unit cell
Length a, b, c (Å)105.575, 105.575, 102.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1313-

NA

21C-1313-

NA

31A-2087-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein MALATE DEHYDROGENASE /


Mass: 32749.783 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CHLOROFLEXUS AURANTIACUS (bacteria) / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P80040, malate dehydrogenase

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Non-polymers , 5 types, 558 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN A, C ENGINEERED MUTATION THR187CYS

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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: 2.52 Å3/Da / Density % sol: 51.16 %
Crystal growpH: 4.5 / Details: 15% PEG400, 100MM NAAC, PH 4.5, 40MM CD2+
Crystal grow
*PLUS
Temperature: 288 K / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
215 %PEG4001reservoir
3100 mMsodium acetate1reservoirpH4.5
440 mM1reservoirCdCl2

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.75→25 Å / Num. obs: 66684 / % possible obs: 96.6 % / Redundancy: 10 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 22.8
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.6 / % possible all: 89
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 25 Å / Redundancy: 10.1 % / Num. measured all: 674394
Reflection shell
*PLUS
% possible obs: 89 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GUY

1guy


Resolution: 1.75→25 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 6551 9.8 %RANDOM
Rwork0.19 ---
obs0.19 58012 96.6 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parametersBiso mean: 20.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4435 0 97 547 5079
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0046
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_deg1.17
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 1.75→1.81 Å / Total num. of bins used: 10 / % reflection obs: 89 %
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.3

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