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- PDB-4cl3: 1.70 A resolution structure of the malate dehydrogenase from Chlo... -

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Basic information

Entry
Database: PDB / ID: 4cl3
Title1.70 A resolution structure of the malate dehydrogenase from Chloroflexus aurantiacus
ComponentsMALATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THERMOPHILE / TRICARBOXYLIC ACID CYCLE
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / carboxylic acid metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
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
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / Malate dehydrogenase
Similarity search - Component
Biological speciesCHLOROFLEXUS SP. Y-400-FL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.699 Å
AuthorsTalon, R. / Madern, D. / Girard, E.
Citation
Journal: Front.Microbiol. / Year: 2014
Title: An Experimental Point of View on Hydration/Solvation in Halophilic Proteins.
Authors: Talon, R. / Coquelle, N. / Madern, D. / Girard, E.
#1: Journal: Mol.Biol.Evol. / Year: 2012
Title: Sampling the Conformational Energy Landscape of a Hyperthermophilic Protein by Engineering Key Substitutions.
Authors: Colletier, J. / Aleksandrov, A. / Coquelle, N. / Mraihi, S. / Mendoza-Barbera, E. / Field, M. / Madern, D.
#2: Journal: J.Mol.Biol. / Year: 2010
Title: Gradual Adaptive Changes of a Protein Facing High Salt Concentrations.
Authors: Coquelle, N. / Talon, R. / Juers, D.H. / Girard, E. / Kahn, R. / Madern, D.
#3: Journal: J.Synchrotron Radia. / Year: 2007
Title: Specific Radiation Damage to Acidic Residues and its Relation to Their Chemical and Structural Environment.
Authors: Fioravanti, E. / Vellieux, F.M.D. / Amara, P. / Madern, D. / Weik, M.
#4: 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.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Gd-Hpdo3A, a Complex to Obtain High-Phasing-Power Heavy-Atom Derivatives for Sad and MAD Experiments: Results with Tetragonal Hen Egg-White Lysozyme.
Authors: Girard, E. / Chantalat, L. / Vicat, J. / Kahn, R.
#6: Journal: J.Synchrotron Radia. / Year: 2011
Title: Using Lanthanoid Complexes to Phase Large Macromolecular Assemblies.
Authors: Talon, R. / Kahn, R. / Dura, M.A. / Maury, O. / Vellieux, F.M.D. / Franzetti, B. / Girard, E.
History
DepositionJan 11, 2014Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 5, 2014ID: 4BGT
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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 / _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
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,48723
Polymers65,4952
Non-polymers1,99221
Water17,024945
1
A: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules

A: MALATE DEHYDROGENASE
D: MALATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,97446
Polymers130,9914
Non-polymers3,98342
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-47.7 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.226, 106.226, 102.566
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-1312-

CD

21A-2017-

HOH

31A-2041-

HOH

41D-2030-

HOH

51D-2034-

HOH

61D-2183-

HOH

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein MALATE DEHYDROGENASE


Mass: 32747.744 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: DSM 63 / Source: (natural) CHLOROFLEXUS SP. Y-400-FL (bacteria) / References: UniProt: B9LLP6, malate dehydrogenase

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Non-polymers , 5 types, 966 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 945 / 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: 2.48 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.6
Details: 4-14% PEG 400, 0.1 M SODIUM ACETATE PH 4.6, 0.04 M CADMIUM ACETATE, 293 K, 1-3 DAYS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2009 / Details: TWO MIRRORS
RadiationMonochromator: DOUBLE CRYSTALS MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→19.7 Å / Num. obs: 68673 / % possible obs: 93.7 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 18.15 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.2 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDS10-05-2010data reduction
SCALA3.3.16data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.699→19.701 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.54 / Stereochemistry target values: ML
Details: ONLY THE A-D PROTEIN HOMODIMER WAS FOUND INSIDE THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT.
RfactorNum. reflection% reflection
Rfree0.2086 3433 5.1 %
Rwork0.1663 --
obs0.1685 67827 91.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 1.699→19.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 60 945 5595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014834
X-RAY DIFFRACTIONf_angle_d1.296574
X-RAY DIFFRACTIONf_dihedral_angle_d13.5311826
X-RAY DIFFRACTIONf_chiral_restr0.082781
X-RAY DIFFRACTIONf_plane_restr0.006854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6994-1.72270.27821330.20592614X-RAY DIFFRACTION94
1.7227-1.74730.24391350.18392649X-RAY DIFFRACTION96
1.7473-1.77330.24991350.1792693X-RAY DIFFRACTION96
1.7733-1.8010.25311370.17642666X-RAY DIFFRACTION96
1.801-1.83050.22571470.17512617X-RAY DIFFRACTION95
1.8305-1.86210.24221330.19192677X-RAY DIFFRACTION95
1.8621-1.89590.32371240.24852526X-RAY DIFFRACTION91
1.8959-1.93240.40791300.34582462X-RAY DIFFRACTION89
1.9324-1.97180.23681210.20082597X-RAY DIFFRACTION92
1.9718-2.01460.2021350.15952597X-RAY DIFFRACTION94
2.0146-2.06140.18161270.14972652X-RAY DIFFRACTION94
2.0614-2.11290.19441540.14862604X-RAY DIFFRACTION94
2.1129-2.170.19361280.16072648X-RAY DIFFRACTION94
2.17-2.23370.23061520.22632405X-RAY DIFFRACTION87
2.2337-2.30570.36361180.28132424X-RAY DIFFRACTION86
2.3057-2.3880.23671640.16282553X-RAY DIFFRACTION93
2.388-2.48340.20691490.14242608X-RAY DIFFRACTION93
2.4834-2.59620.1721340.13642604X-RAY DIFFRACTION93
2.5962-2.73280.18171480.13952554X-RAY DIFFRACTION92
2.7328-2.90350.19611310.14882573X-RAY DIFFRACTION92
2.9035-3.12680.2181370.14672585X-RAY DIFFRACTION91
3.1268-3.440.18171450.1432551X-RAY DIFFRACTION90
3.44-3.93430.16461410.13942511X-RAY DIFFRACTION89
3.9343-4.94390.14481420.13172509X-RAY DIFFRACTION88
4.9439-19.70230.21521330.16732515X-RAY DIFFRACTION84
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)
11.65620.1176-1.04920.4417-0.38020.97080.0050.0283-0.0896-0.0660.02050.06750.08850.0125-0.0220.1772-0.0063-0.00520.1622-0.02750.208-21.538229.63925.2104
20.45350.60560.06862.04010.54853.59930.3589-0.7695-0.36390.47570.0229-0.31980.19390.0159-0.28920.43760.22470.01090.8686-0.00470.88765.079523.315.9523
30.74830.40640.19871.05030.66821.3466-0.03530.1225-0.1397-0.12040.0412-0.15340.07180.0994-0.01290.12620.02030.02370.13310.0030.1371-3.803640.25455.8699
40.9762-0.05510.22110.7576-0.11561.1215-0.06190.0535-0.0605-0.09550.0002-0.14120.04460.13250.06480.12370.01160.03430.13110.00060.1553-0.018643.78348.3169
52.737-1.65060.22431.0122-0.25450.9936-0.22670.3952-0.8088-0.4452-0.11990.00320.6090.04690.30330.4460.00660.1740.3027-0.09230.6338.330928.379-6.8034
61.27110.5280.37081.17220.65270.86420.005-0.12110.02730.1177-0.01880.0878-0.0054-0.09410.00730.1490.00510.02590.14590.00510.1249-36.017457.485929.5986
73.13522.276-1.00155.26030.06691.6229-0.12460.87710.7636-1.45390.34140.4349-0.5760.1526-0.17330.66180.0223-0.0740.363-0.00350.5954-28.579485.836227.8852
80.8934-0.0765-0.4370.62740.19761.2287-0.0123-0.09220.13960.07460.0016-0.0191-0.0956-0.03790.00270.12690.0078-0.01840.1153-0.00680.13-18.110967.309126.1349
90.48080.08810.10960.6311-0.32421.0732-0.0264-0.07240.10150.0448-0.0335-0.0823-0.10560.05450.06270.115-0.0022-0.0080.1042-0.00990.141-13.381468.795723.5414
102.58732.4744-0.48132.71770.05642.28330.3179-0.53010.77940.43050.00970.0256-0.4401-0.1729-0.31980.36890.01560.00130.2679-0.1570.4095-20.765784.459739.4394
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:78)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 79:92)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 93:193)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 194:304)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 305:309)
6X-RAY DIFFRACTION6(CHAIN D AND RESID 1:78)
7X-RAY DIFFRACTION7(CHAIN D AND RESID 79:92)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 93:193)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 194:304)
10X-RAY DIFFRACTION10(CHAIN D AND RESID 305:309)

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