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- PDB-6ka1: E.coli Malate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6ka1
TitleE.coli Malate dehydrogenase
ComponentsMalate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / Dehydrogenase
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity ...malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / anaerobic respiration / extrinsic component of membrane / tricarboxylic acid cycle / glycolytic process / oxidoreductase activity / protein homodimerization activity / membrane / cytosol / cytoplasm
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / 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 speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.543 Å
AuthorsWang, H. / Wang, M. / Sun, H.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)17307017 Hong Kong
CitationJournal: To Be Published
Title: MDH is a major silver target in E. coli
Authors: Wang, H. / Wang, M. / Sun, H.
History
DepositionJun 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)130,4454
Polymers130,4454
Non-polymers00
Water19,2221067
1
A: Malate dehydrogenase
C: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)65,2232
Polymers65,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-24 kcal/mol
Surface area22730 Å2
MethodPISA
2
B: Malate dehydrogenase
D: Malate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)65,2232
Polymers65,2232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-23 kcal/mol
Surface area22660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.935, 125.102, 85.756
Angle α, β, γ (deg.)90.000, 107.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Malate dehydrogenase


Mass: 32611.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The first G comes from the purification Tag. / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: mdh / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61889, malate dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1067 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG3350 20%, DL-Malic acid 0.1M (pH 5.5) / PH range: 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1.0401 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2018
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0401 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 158413 / % possible obs: 92.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Χ2: 0.914 / Net I/σ(I): 17 / Num. measured all: 1038999
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.54-1.576.50.7772570.8230.3180.8350.82185.2
1.57-1.66.60.68775400.8610.2790.7430.83688.4
1.6-1.636.60.5877110.8870.2360.6270.86490.6
1.63-1.666.50.49377730.9090.2020.5340.86391
1.66-1.696.50.39978320.9340.1640.4330.88191.9
1.69-1.736.40.33778530.9460.140.3660.88592.5
1.73-1.786.30.2679490.9610.110.2830.91493.2
1.78-1.836.10.20379300.9710.0870.2210.92793.3
1.83-1.8860.1676000.9770.0690.1750.99389.1
1.88-1.946.40.12678020.9840.0530.1371.04691
1.94-2.016.60.09881040.9890.040.1061.00995.5
2.01-2.096.60.07981610.9910.0330.0861.02195.8
2.09-2.196.50.06582310.9930.0270.0711.02396.3
2.19-2.36.50.05682610.9940.0230.060.98796.5
2.3-2.446.50.04981370.9940.0210.0530.93295.3
2.44-2.636.40.04477090.9940.0180.0480.89190.3
2.63-2.970.04180220.9950.0160.0440.89193.6
2.9-3.327.30.03784030.9960.0150.040.88398.2
3.32-4.187.20.03383580.9970.0130.0360.77697.2
4.18-506.90.03877800.9950.0160.0410.85989.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260:000refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KKA
Resolution: 1.543→37.166 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.37
RfactorNum. reflection% reflection
Rfree0.1817 7872 5 %
Rwork0.1565 --
obs0.1578 157588 92.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.92 Å2 / Biso mean: 18.9185 Å2 / Biso min: 5.11 Å2
Refinement stepCycle: final / Resolution: 1.543→37.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8841 0 0 1067 9908
Biso mean---30.98 -
Num. residues----1227
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5427-1.56020.23452510.19184255450679
1.5602-1.57860.23692470.18234608485585
1.5786-1.59780.2082410.17754731497288
1.5978-1.61810.19252420.16954833507589
1.6181-1.63930.20322380.17044815505389
1.6393-1.66180.18952420.16594899514190
1.6618-1.68550.20082240.16484939516391
1.6855-1.71070.20342590.16094909516891
1.7107-1.73740.21082610.16064931519292
1.7374-1.76590.18972910.16064999529092
1.7659-1.79640.2062700.16464976524693
1.7964-1.8290.18932570.16355020527793
1.829-1.86420.19582470.16414987523491
1.8642-1.90230.18962040.16774564476884
1.9023-1.94360.192610.15675150541194
1.9436-1.98880.18872750.15935145542095
1.9888-2.03860.19752550.15615171542696
2.0386-2.09370.19792810.15045175545696
2.0937-2.15530.17612770.14825210548796
2.1553-2.22480.18362570.14595240549797
2.2248-2.30430.16072630.15225235549896
2.3043-2.39660.19212950.15955155545096
2.3966-2.50560.19173030.15915116541995
2.5056-2.63770.18052500.16064766501688
2.6377-2.80290.18382430.16244944518791
2.8029-3.01920.19892950.16595320561598
3.0192-3.32290.17422830.15265338562198
3.3229-3.80330.162950.14275301559698
3.8033-4.79020.15422830.13565088537193
4.7902-37.17690.16442820.16684896517889
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.52740.4286-0.05511.7117-0.29112.273-0.02830.1363-0.0371-0.07010.0815-0.03080.05130.1963-0.03390.0416-0.00460.00080.0903-0.02380.068117.5941-7.77216.9316
21.5770.4590.17251.6999-0.06963.57660.0627-0.0035-0.1040.08280.0239-0.0640.25620.069-0.05080.09390.0104-0.01060.0689-0.01830.07214.683-15.760818.9987
32.2557-0.4175-0.25991.88750.28272.01570.0959-0.0688-0.08290.16660.01920.05030.08130.0896-0.01320.0621-0.01350.00410.11490.00160.087118.7166-5.370127.0813
42.6531-0.7092-1.14972.52431.12563.1284-0.0365-0.2173-0.19540.37410.0457-0.01640.28740.133-0.01010.1283-0.0144-0.03150.10850.02130.070320.7794-5.743136.0735
51.1002-0.07270.24121.8063-0.06240.9992-0.02750.05030.00630.07310.0307-0.0333-0.070.2260.00370.0386-0.0375-0.00140.1059-0.00570.055221.48125.582926.9811
61.10470.18920.6881.08390.53771.3536-0.22440.290.1663-0.2990.10890.2289-0.22290.03450.09360.1795-0.083-0.04480.14630.0350.138414.410620.183918.8282
71.78631.70080.93552.44340.34421.7171-0.1745-0.05880.48010.1637-0.21990.5322-0.0476-0.28110.21260.1271-0.0390.01940.166-0.0660.25984.175918.777425.4026
87.4688-1.0401-1.48141.11660.5620.97460.0647-0.23-0.02190.103-0.03090.0070.03870.125-0.04480.0751-0.0388-0.01290.119-0.00230.07614.02832.573618.9434
91.2738-0.731-0.7541.03460.10271.40310.00530.18280.0415-0.08850.017-0.2407-0.29820.1404-0.08520.0781-0.08180.01310.16960.00370.110627.689111.509923.6402
100.8285-0.45280.3092.63210.06370.12930.0428-0.01630.05180.2349-0.033-0.0992-0.17750.1064-0.01960.1192-0.0617-0.01160.1062-0.00090.086923.695915.916731.8495
110.48050.0705-0.08941.42030.65651.13980.02330.0556-0.0022-0.01260.0223-0.171-0.00190.0275-0.04070.07110.018-0.00030.06880.00360.07039.865-6.419654.4462
121.238-0.3399-0.04411.35950.15410.7048-0.00850.1286-0.1646-0.0154-0.03620.17460.0568-0.12410.02330.084-0.00410.00220.0955-0.02950.0857-5.3257-20.053448.2688
131.59180.3225-0.07031.25350.63070.49690.0011-0.07440.0730.0473-0.13790.16850.0297-0.17110.06920.0465-0.02650.00380.1132-0.0220.0822-1.69781.948812.0543
141.69370.0598-0.39110.1940.1050.80780.0017-0.09210.2233-0.0498-0.15530.2668-0.1713-0.19390.03250.0682-0.0076-0.0090.1561-0.03450.1643-7.59196.001110.5256
152.8143-0.23660.19181.8358-0.59031.88490.1414-0.3405-0.1630.1636-0.17090.33690.2381-0.3383-0.0610.0727-0.0920.0070.2612-0.07330.1526-14.2423-9.04289.2248
162.4804-0.61730.26831.29470.37541.25120.01180.0031-0.0207-0.0816-0.05130.12930.0953-0.12890.01410.0929-0.0259-0.01850.0844-0.02650.058-5.7723-12.64620.2452
171.4158-0.11890.23640.95960.88411.34470.15030.1948-0.20260.1234-0.0237-0.03440.26940.1841-0.0770.2170.0371-0.02560.1219-0.03290.14059.0108-24.0027-0.1021
181.7339-1.14481.7674.2979-3.10136.15640.0243-0.03390.0051-0.11130.1280.05810.2916-0.0335-0.08510.0753-0.0159-0.00020.1029-0.01860.09212.9504-8.68356.0732
192.0799-0.0395-0.16481.9807-0.35391.11640.02430.4612-0.097-0.5127-0.0063-0.115-0.040.1478-0.01230.2051-0.00750.00170.1818-0.01770.0642-4.0942-12.8351-8.8072
201.4162-1.9473-0.15544.68310.33930.02540.18140.52620.0062-0.5314-0.1882-0.1606-0.10170.16950.02330.35940.0572-0.01970.3194-0.04270.1159-1.7222-13.3012-13.4876
213.6544-1.6107-1.82881.87380.83751.72530.07460.228-0.4460.0068-0.0420.20930.4692-0.16240.06910.26-0.0927-0.06840.1797-0.05340.2036-10.0524-26.6618-2.6027
220.6999-0.44110.3331.68570.8160.9097-0.01110.11690.03130.0162-0.03760.1609-0.0371-0.09380.03670.07810.02230.01940.11820.0150.0744-12.72034.541551.9031
231.70160.8945-0.26011.54460.28931.51750.01130.30630.2493-0.2889-0.04450.1273-0.2048-0.17450.0640.14730.06080.0170.1910.04950.1584-14.397415.8350.0324
245.09572.1716-1.36962.2474-0.00761.8059-0.080.27960.3798-0.2487-0.0244-0.1056-0.4112-0.04710.12340.22820.05250.00960.19020.09920.2041-8.860924.853349.5539
251.4019-0.53980.34341.2519-0.35031.1562-0.0650.12540.28320.10840.01470.0089-0.2674-0.02980.05870.13930.02280.00590.05450.01190.1235-7.255619.954363.581
260.6616-0.19930.28831.27180.04852.1472-0.1337-0.03770.14090.173-0.0206-0.1587-0.31960.16560.1190.1473-0.007-0.03870.08730.00630.15647.523214.19471.6412
278.1367-1.2293-2.14440.2060.41811.158-0.0676-0.13650.02070.2080.02190.18070.023-0.06440.060.13010.02940.0510.0813-0.0010.1291-10.13018.777964.8534
281.57430.5771-0.24772.2227-0.0960.8422-0.1076-0.23740.19310.47230.0536-0.0303-0.155-0.1399-0.0210.31580.0858-0.00720.0731-0.03030.1758-10.285121.657772.2536
296.14881.56423.56950.6390.71512.4588-0.0931-0.35640.16290.57450.1023-0.0084-0.0343-0.12380.02380.41020.16470.0580.1825-0.05790.2219-11.683620.694677.2237
300.2999-0.11440.08170.7372-0.26250.6681-0.03170.00590.29150.21920.1467-0.094-0.17030.00240.24450.5018-0.0232-0.2098-0.030.03480.41561.196531.424967.7914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 43 )A10 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 73 )A44 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 99 )A74 - 99
4X-RAY DIFFRACTION4chain 'A' and (resid 100 through 118 )A100 - 118
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 172 )A119 - 172
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 205 )A173 - 205
7X-RAY DIFFRACTION7chain 'A' and (resid 206 through 226 )A206 - 226
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 252 )A227 - 252
9X-RAY DIFFRACTION9chain 'A' and (resid 253 through 281 )A253 - 281
10X-RAY DIFFRACTION10chain 'A' and (resid 282 through 321 )A282 - 321
11X-RAY DIFFRACTION11chain 'B' and (resid 5 through 118 )B5 - 118
12X-RAY DIFFRACTION12chain 'B' and (resid 119 through 321 )B119 - 321
13X-RAY DIFFRACTION13chain 'C' and (resid 10 through 58 )C10 - 58
14X-RAY DIFFRACTION14chain 'C' and (resid 59 through 81 )C59 - 81
15X-RAY DIFFRACTION15chain 'C' and (resid 82 through 118 )C82 - 118
16X-RAY DIFFRACTION16chain 'C' and (resid 119 through 172 )C119 - 172
17X-RAY DIFFRACTION17chain 'C' and (resid 173 through 226 )C173 - 226
18X-RAY DIFFRACTION18chain 'C' and (resid 227 through 252 )C227 - 252
19X-RAY DIFFRACTION19chain 'C' and (resid 253 through 281 )C253 - 281
20X-RAY DIFFRACTION20chain 'C' and (resid 282 through 295 )C282 - 295
21X-RAY DIFFRACTION21chain 'C' and (resid 296 through 321 )C296 - 321
22X-RAY DIFFRACTION22chain 'D' and (resid 10 through 68 )D10 - 68
23X-RAY DIFFRACTION23chain 'D' and (resid 69 through 97 )D69 - 97
24X-RAY DIFFRACTION24chain 'D' and (resid 98 through 118 )D98 - 118
25X-RAY DIFFRACTION25chain 'D' and (resid 119 through 172 )D119 - 172
26X-RAY DIFFRACTION26chain 'D' and (resid 173 through 234 )D173 - 234
27X-RAY DIFFRACTION27chain 'D' and (resid 235 through 253 )D235 - 253
28X-RAY DIFFRACTION28chain 'D' and (resid 254 through 281 )D254 - 281
29X-RAY DIFFRACTION29chain 'D' and (resid 282 through 295 )D282 - 295
30X-RAY DIFFRACTION30chain 'D' and (resid 296 through 321 )D296 - 321

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