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- PDB-4jco: 1.7 A resolution structure of wild type malate dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 4jco
Title1.7 A resolution structure of wild type malate dehydrogenase from haloarcula marismortui
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / HALOPHILE / MALATE DEHYDROGENASE TRICARBOXYLIC ACID CYCLE
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 / FOURIER, DIFFERENCE FOURIER / Resolution: 1.7 Å
AuthorsVellieux, F.M.D.
Citation
Journal: To be Published
Title: 1.7 A resolution structure of wild type malate dehydrogenase from haloarcula marismortui
Authors: Vellieux, F.M.D.
#1: Journal: J Synchrotron Radiat / Year: 2007
Title: Specific radiation damage to acidic residues and its relation to their chemical and structural environment.
Authors: Fioravanti, E. / Vellieux, F.M. / Amara, P. / Madern, D. / Weik, M.
#2: 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.
#3: 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.
#4: Journal: Science / Year: 1995
Title: Structural features that stabilize halophilic malate dehydrogenase from an archaebacterium.
Authors: Dym, O. / Mevarech, M. / Sussman, J.L.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_PDB_ins_code / _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_alt_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.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_PDB_ins_code / _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_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr1_label_alt_id / _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: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,41043
Polymers131,3514
Non-polymers1,05939
Water26,4461468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17580 Å2
ΔGint-441 kcal/mol
Surface area41780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.813, 114.065, 124.022
Angle α, β, γ (deg.)90.00, 93.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-760-

HOH

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Components

#1: Protein
Malate dehydrogenase


Mass: 32837.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui (Halophile) / Strain: HMS174 / Gene: mdh, rrnAC2706 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07841, malate dehydrogenase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1468 / 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: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 58% MPD, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.939
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 25, 2005 / Details: MIRRORS
RadiationMonochromator: SILICON (1 1 1) CHANNEL-CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.7→123.792 Å / Num. obs: 192220 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.52
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.79 % / Rmerge(I) obs: 1.224 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER, DIFFERENCE FOURIER
Starting model: PDB ENTRY 2J5K

2j5k


Resolution: 1.7→42.964 Å / SU ML: 0.24 / σ(F): 1.99 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.257 9607 5 %RANDOM
Rwork0.224 ---
obs0.2257 192185 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→42.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9204 0 39 1468 10711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089505
X-RAY DIFFRACTIONf_angle_d1.17512955
X-RAY DIFFRACTIONf_dihedral_angle_d13.6173517
X-RAY DIFFRACTIONf_chiral_restr0.081437
X-RAY DIFFRACTIONf_plane_restr0.0061792
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.71930.36983200.32746090100
1.7193-1.73950.34443210.3256106100
1.7395-1.76080.32483170.30876014100
1.7608-1.7830.31173200.30066090100
1.783-1.80650.33943230.30256127100
1.8065-1.83130.343150.29265994100
1.8313-1.85740.33183230.28536131100
1.8574-1.88510.32153180.27366045100
1.8851-1.91460.29653210.26626088100
1.9146-1.9460.30723210.25446100100
1.946-1.97950.27883200.23916086100
1.9795-2.01550.26943180.24026049100
2.0155-2.05430.27593210.23956099100
2.0543-2.09620.29653190.23486045100
2.0962-2.14180.29383220.23116120100
2.1418-2.19160.28543200.2293608699
2.1916-2.24640.27923190.22866062100
2.2464-2.30720.25723190.2256607399
2.3072-2.37510.25543210.2288609599
2.3751-2.45170.25663180.2284604499
2.4517-2.53930.27253180.2265604399
2.5393-2.6410.25563190.225606899
2.641-2.76120.25013210.2223608999
2.7612-2.90670.27153200.21776088100
2.9067-3.08880.2513200.2095608399
3.0888-3.32720.24823220.21296107100
3.3272-3.66190.24013220.20066132100
3.6619-4.19130.19493220.18186116100
4.1913-5.27910.193240.1756614799
5.2791-42.97780.2183230.2102616199
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)
10.7705-0.3442-1.09410.63590.51162.20340.05250.04580.0738-0.1138-0.10420.0491-0.4446-0.15640.05770.2680.0119-0.02380.1753-0.05670.156213.456620.678535.4858
27.2169-0.77221.11532.0691.5465.3094-0.01960.26280.0560.1467-0.10490.36510.0668-0.52010.0650.22020.0347-0.00820.3298-0.10350.2166-0.713319.013939.4854
31.039-0.67840.12841.3056-0.11.0758-0.0427-0.0076-0.00410.1507-0.06510.0489-0.0709-0.06720.08890.2226-0.02990.02280.1675-0.06680.09819.15529.037552.0984
40.2448-0.21730.20922.4835-0.5743.3768-0.1057-0.28440.11440.91610.0339-0.4259-0.53580.25680.0770.4081-0.0407-0.04860.3376-0.08630.238932.180712.171961.535
52.11131.47430.36153.15711.05610.9975-0.02620.04110.13730.12720.07040.0399-0.30510.07670.00060.2651-0.01060.0090.1504-0.02930.095921.401812.822541.9997
61.7911-0.6095-0.00782.1196-0.00222.1032-0.0402-0.2204-0.10090.4329-0.04090.12860.287-0.18060.10840.3207-0.04670.05930.2573-0.04620.150811.40855.305557.8331
70.5041-0.8192-0.65662.4922.7883.40450.1067-0.04780.08410.1732-0.11180.1945-0.3057-0.310.80730.5052-0.06680.24830.3835-0.27870.51181.756521.635260.249
81.91310.8671-0.42070.7365-0.19510.6990.0698-0.16880.130.2402-0.1404-0.0205-0.31990.25110.06150.2172-0.0679-0.04280.1816-0.01110.152638.644217.309439.1604
95.7693-2.58762.16251.2727-0.95123.6681-0.07110.26120.4070.75860.32250.1515-0.7834-0.68110.07441.62790.49320.36511.03510.03540.698734.666238.448326.8648
106.3117-3.93643.39766.2468-4.33568.93650.0253-0.59570.50250.1681-0.1576-0.5157-1.29680.01210.11020.536-0.15720.01130.31880.01160.288146.218632.530625.7495
117.00341.8063.75860.81890.19553.70920.42310.5762-0.2421-0.06770.4594-1.0525-0.2221.0372-0.50670.3236-0.16310.08820.7446-0.10570.69155.618117.972633.8611
121.38250.66290.46170.42670.47311.2497-0.0024-0.05860.0696-0.0507-0.0492-0.0726-0.12160.12070.06450.217-0.03560.00610.12390.02110.152933.732518.301615.754
130.5322-0.0703-0.13641.7683-0.21912.2908-0.0430.01630.1899-0.04970.0130.0862-0.521-0.21660.06360.3358-0.0214-0.00760.15680.00850.223324.420622.827217.7367
140.38550.2627-0.15451.9134-0.60751.7224-0.01410.03420.0589-0.021-0.0228-0.2027-0.24270.2850.03630.2293-0.04550.0270.18690.01560.182142.305818.281310.9969
152.05560.39880.89411.03550.33982.27270.0136-0.1129-0.12480.172-0.08090.05290.2567-0.18320.06640.2154-0.02530.05290.1461-0.02680.124815.407-19.285129.2082
163.6445-1.4128-3.33292.84282.81957.8304-0.0356-0.0383-0.0275-0.16370.01390.05350.45710.04360.04710.3003-0.06010.01220.1827-0.04320.22369.2519-26.087312.2141
171.10710.6544-0.32560.9072-0.31840.6757-0.07290.1427-0.0388-0.16640.00220.01220.0281-0.07220.06870.1708-0.00170.01170.138-0.04420.109921.4135-9.5588.6454
180.69120.5706-0.66032.1308-2.58563.9205-0.03250.1305-0.1411-0.6721-0.0525-0.17650.50170.36630.09440.40330.04130.06860.2287-0.04060.180935.1393-14.63913.0663
191.8616-1.27511.11341.8539-1.2990.9565-0.016-0.0149-0.02120.1274-0.04560.0907-0.0347-0.07380.04650.2149-0.01420.02390.1422-0.03840.09220.122-8.59919.5633
202.13090.6912-0.60412.0476-0.34983.5442-0.09020.2531-0.0067-0.314-0.02740.1031-0.3304-0.14290.08470.19140.0131-0.02510.1593-0.03960.113114.0649-5.09752.0285
213.3799-1.1466-0.29432.85252.1515.17260.1499-0.003-0.2345-0.5273-0.42050.3960.4078-0.29110.28910.4813-0.02670.00940.2787-0.10650.19649.6792-20.5665-2.8873
222.3774-1.12991.23141.9026-0.7492.0084-0.01350.1108-0.0978-0.0688-0.066-0.08050.12160.21020.07370.12320.00630.03670.13890.00890.102938.0485-16.055322.668
233.53640.2080.56160.03040.26913.0736-0.11520.57030.1106-0.181-0.1008-0.25260.07840.60380.11560.12970.03380.06270.25770.0680.217747.9549-15.502723.9826
241.4272.4824-2.72764.3192-4.74475.21220.5539-0.369-0.5160.0018-0.05930.66821.7908-1.0282-0.32960.8526-0.1595-0.24260.39590.12140.536639.1317-33.884334.7596
253.03870.4599-1.73954.2307-1.63933.6265-0.14720.4859-0.25530.13410.22290.17120.91250.12620.23270.37080.09020.03110.37660.03880.284549.5423-28.882835.8071
261.52-0.93380.08331.08090.14361.3246-0.0604-0.0306-0.0930.1609-0.0015-0.02970.13290.07950.05870.2327-0.01710.0090.11570.02990.135931.9984-18.632947.3347
271.87150.76090.69191.87710.49531.7955-0.0711-0.0018-0.09290.01780.0636-0.00870.28060.09150.05160.15670.03430.03240.10150.02340.130831.333-17.505937.1911
281.2047-0.8679-0.19842.5392-0.78072.6002-0.1016-0.1834-0.01090.2066-0.0745-0.1910.13050.32730.14630.2313-0.0079-0.0230.21910.05040.16642.5441-19.554853.4432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 22:119)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 120:132)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 133:212)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 219:238)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 239:266)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 267:325)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 326:330)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 22:98)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 99:106)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 107:128)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 129:132)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 133:212)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 219:259)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 260:330)
15X-RAY DIFFRACTION15(CHAIN C AND RESID 22:100)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 101:132)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 133:212)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 219:244)
19X-RAY DIFFRACTION19(CHAIN C AND RESID 245:270)
20X-RAY DIFFRACTION20(CHAIN C AND RESID 271:319)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 320:330)
22X-RAY DIFFRACTION22(CHAIN D AND RESID 22:76)
23X-RAY DIFFRACTION23(CHAIN D AND RESID 77:95)
24X-RAY DIFFRACTION24(CHAIN D AND RESID 96:106)
25X-RAY DIFFRACTION25(CHAIN D AND RESID 107:132)
26X-RAY DIFFRACTION26(CHAIN D AND RESID 132:233)
27X-RAY DIFFRACTION27(CHAIN D AND RESID 234:270)
28X-RAY DIFFRACTION28(CHAIN D AND RESID 271:330)

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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