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- PDB-2x0r: R207S, R292S Mutant of Malate Dehydrogenase from the Halophilic A... -

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Basic information

Entry
Database: PDB / ID: 2x0r
TitleR207S, R292S Mutant of Malate Dehydrogenase from the Halophilic Archeon Haloarcula marismortui (HoloForm)
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / PROTEIN-SOLVENT INTERACTION / HAOPHILIC / ION-BINDING / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / L-lactate dehydrogenase (NAD+) activity / lactate 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Malate dehydrogenase
Similarity search - Component
Biological speciesHALOARCULA MARISMORTUI (Halophile)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.915 Å
AuthorsIrimia, A. / Ebel, C. / Vellieux, F.M.D. / Richard, S.B. / Cosenza, L.W. / Zaccai, G. / Madern, D.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The Oligomeric States of Haloarcula Marismortui Malate Dehydrogenase are Modulated by Solvent Components as Shown by Crystallographic and Biochemical Studies
Authors: Irimia, A. / Ebel, C. / Madern, D. / Richard, S.B. / Cosenza, L.W. / Zaccai, G. / Vellieux, F.M.D.
#1: Journal: Biochemistry / Year: 2000
Title: Insights Into the Molecular Relationships between Malate and Lactate Dehydrogenases: Structural and Biochemical Properties of Monomeric and Dimeric Intermediates of a Mutant of Tetrameric L- ...Title: Insights Into the Molecular Relationships between Malate and Lactate Dehydrogenases: Structural and Biochemical Properties of Monomeric and Dimeric Intermediates of a Mutant of Tetrameric L-[Ldh-Like] Malate Dehydrogenase from the Halophilic Archaeon Haloarcula Marismortui
Authors: Madern, D. / Ebel, C. / Mevarech, M. / Richard, S.B. / Pfister, C. / Zaccai, G.
#2: 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.
#3: Journal: Science / Year: 1995
Title: Structural Features that Stabilize Halophilic Malate Dehydrogenase from an Archaebacterium
Authors: Dym, O. / Mevarech, M. / Sussman, J.L.
#4: Journal: Eur.J.Biochem. / Year: 1995
Title: Mutation at a Single Acidic Amino Acid Enhances the Halophilic Behaviour of Malate Dehydrogenase from Haloarcula Marismortui in Physiological Salts
Authors: Madern, D. / Pfister, C. / Zaccai, G.
#5: 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
DepositionDec 17, 2009Deposition site: PDBE / Processing site: PDBE
SupersessionDec 29, 2009ID: 1GT2
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Database references / Structure summary
Category: citation / struct / Item: _citation.page_last / _struct.title
Revision 1.4Dec 20, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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 / _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)66,97913
Polymers65,3952
Non-polymers1,58411
Water2,162120
1
A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
B: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,95726
Polymers130,7904
Non-polymers3,16722
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area18390 Å2
ΔGint-262.54 kcal/mol
Surface area41810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.360, 125.910, 125.840
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: 32697.496 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOARCULA MARISMORTUI (Halophile) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 188 TO SER ENGINEERED RESIDUE IN CHAIN A, ARG 267 TO SER ...ENGINEERED RESIDUE IN CHAIN A, ARG 188 TO SER ENGINEERED RESIDUE IN CHAIN A, ARG 267 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 188 TO SER ENGINEERED RESIDUE IN CHAIN B, ARG 267 TO SER
Sequence detailsR207S,R292S MUTANT

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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: 3.5 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 7.6 / Details: 2 M NACL, 25 MM TRIS PH 7.6, 2.5 MM NADH, 50% MPD

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: NONIUS / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 21, 2000 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.91→44.72 Å / Num. obs: 20001 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 5.03 % / Biso Wilson estimate: 35.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.9→3.01 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
BIOMOLdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HLP

2hlp


Resolution: 2.915→44.504 Å / SU ML: 0.41 / σ(F): 1.46 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2864 964 4.8 %
Rwork0.1839 --
obs0.1888 19986 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.2 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 43.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.8083 Å20 Å2-0 Å2
2--8.7394 Å20 Å2
3----6.2192 Å2
Refinement stepCycle: LAST / Resolution: 2.915→44.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4582 0 97 120 4799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084780
X-RAY DIFFRACTIONf_angle_d1.4016517
X-RAY DIFFRACTIONf_dihedral_angle_d23.8871813
X-RAY DIFFRACTIONf_chiral_restr0.117727
X-RAY DIFFRACTIONf_plane_restr0.007883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9152-3.06880.37721370.25192646X-RAY DIFFRACTION97
3.0688-3.26110.37441270.23962686X-RAY DIFFRACTION99
3.2611-3.51280.33411360.20162699X-RAY DIFFRACTION98
3.5128-3.86610.29111380.17472698X-RAY DIFFRACTION98
3.8661-4.42510.251240.13462707X-RAY DIFFRACTION98
4.4251-5.57340.21621450.14022769X-RAY DIFFRACTION99
5.5734-44.50870.27071570.18522817X-RAY DIFFRACTION98
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3341-0.1449-0.43991.5626-0.62640.5593-0.2444-0.1908-0.22660.03430.0207-0.26760.10660.04190.23720.06870.04280.046-0.01750.08520.073518.344216.909330.3643
20.64210.30750.34650.1660.260.6633-0.1196-0.0083-0.41850.41570.26480.01420.04170.129-0.0970.32360.10990.22180.0618-0.00950.296822.648210.263413.2445
30.778-0.75350.32351.1256-0.04820.7362-0.16580.2342-0.2620.1321-0.02470.1652-0.10630.1360.13790.1605-0.04540.15030.1985-0.01870.184710.826618.806110.4639
40.6786-0.455-0.48980.80360.14560.4223-0.23290.09070.120.09570.1775-0.17920.166-0.03390.05280.2199-0.08260.04770.0501-0.01770.10096.672732.74414.1434
50.152-0.1880.2290.2264-0.35370.5838-0.20590.0947-0.0242-0.1436-0.0563-0.17070.14180.07410.1260.1001-0.01160.14570.001-0.12510.08858.315317.16157.7704
60.0885-0.0568-0.03350.04560.00720.0337-0.15290.15440.1385-0.0501-0.1075-0.0508-0.0810.00820.15110.232-0.284-0.0099-0.11340.19630.194516.531441.672522.8491
70.1663-0.1749-0.23270.63890.32630.33990.0201-0.097-0.0978-0.02590.09120.05630.11890.1477-0.09830.16690.14530.04920.19660.04290.426637.626539.487436.6601
81.42030.49620.61030.31850.2950.5571-0.2860.1831-0.0238-0.08460.1352-0.0046-0.37160.15660.18590.2251-0.1473-0.10790.09610.07650.14923.847650.036438.0587
90.72780.1291-0.08550.10130.12170.245-0.2325-0.04530.21540.09630.11440.02310.06930.04890.10110.11870.0162-0.01820.0950.01860.152816.444726.506749.8343
100.43590.0929-0.05680.1171-0.15350.4907-0.2603-0.1062-0.17360.0554-0.0461-0.2308-0.0530.31830.1846-0.07950.075-0.19340.25650.1219-0.029520.211537.542148.4033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:97)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 98:143)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 144:180)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 181:239)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 240:330)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 22:97)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 98:109)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 110:167)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 168:211)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 212:330)

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