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- PDB-6ka0: Silver-bound E.coli Malate dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6ka0
TitleSilver-bound E.coli Malate dehydrogenase
ComponentsMalate dehydrogenase
KeywordsCYTOSOLIC PROTEIN / silver nano-particle / dehydrogenase / glyoxylate cycle
Function / homology
Function and homology information


malate dehydrogenase activity / fermentation / malate dehydrogenase / L-malate dehydrogenase 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 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
SILVER ION / Malate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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 ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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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)130,50113
Polymers129,4734
Non-polymers1,0289
Water181
1
A: Malate dehydrogenase
C: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3047
Polymers64,7362
Non-polymers5685
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-32 kcal/mol
Surface area22500 Å2
MethodPISA
2
B: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1966
Polymers64,7362
Non-polymers4604
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-26 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.860, 152.830, 78.500
Angle α, β, γ (deg.)90.000, 108.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Malate dehydrogenase /


Mass: 32368.176 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Dimer or tetramer in solution / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: mdh / Plasmid: pRHis-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61889, malate dehydrogenase
#2: Chemical
ChemComp-AG / SILVER ION / Silver


Mass: 107.868 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.88 %
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 / Temp details: Room temprature

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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: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2018
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.22→50.94 Å / Num. obs: 55114 / % possible obs: 98.6 % / Redundancy: 3.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.042 / Rrim(I) all: 0.083 / Net I/σ(I): 12.2 / Num. measured all: 211450 / Scaling rejects: 53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.22-2.283.80.6821546440170.7140.40.7942.198.3
9.93-50.943.70.03223856420.9980.0180.03733.498.1

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Processing

Software
NameVersionClassification
Aimless0.7.2data scaling
PHENIX1.14_3260:000refinement
PDB_EXTRACT3.25data extraction
xia22data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KKA

5kka


Resolution: 2.22→48.161 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.7
RfactorNum. reflection% reflection
Rfree0.2716 2728 4.95 %
Rwork0.2195 --
obs0.2221 55057 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.63 Å2 / Biso mean: 59.8502 Å2 / Biso min: 24.66 Å2
Refinement stepCycle: final / Resolution: 2.22→48.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8744 0 37 1 8782
Biso mean--56.7 60.61 -
Num. residues----1211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.22-2.26040.38691520.32192726287898
2.2604-2.30390.40651320.31912761289398
2.3039-2.35090.34351490.30392686283598
2.3509-2.4020.34041440.28612754289898
2.402-2.45790.32411370.29112745288297
2.4579-2.51930.32171510.27532632278395
2.5193-2.58740.37841510.28082742289399
2.5874-2.66360.35611450.270127872932100
2.6636-2.74950.31881360.270327662902100
2.7495-2.84780.33141420.259428032945100
2.8478-2.96180.2941680.271928072975100
2.9618-3.09660.35291220.259327532875100
3.0966-3.25980.32981310.254128162947100
3.2598-3.4640.29211420.23662770291299
3.464-3.73140.2721640.21352763292799
3.7314-4.10670.23331560.18752737289398
4.1067-4.70050.21281410.16642675281696
4.7005-5.92040.23091340.1822786292098
5.9204-48.17220.17291310.1582820295199
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)
10.60810.08440.10270.77590.43081.21230.21440.0775-0.0985-0.1203-0.0751-0.88050.0362-0.0749-0.1660.17550.00640.05270.30880.07480.5722-1.28421.011614.8528
20.6645-1.12430.11282.52810.63821.10790.32910.20180.0885-0.07540.0177-0.53660.0714-0.1286-0.10580.14750.091-0.1680.28370.20990.81434.510119.606723.0917
31.13280.1293-0.00720.27560.26011.94310.1449-0.2087-0.09980.18550.0191-0.58610.57340.0691-0.04860.48950.0657-0.33880.26670.12290.99635.142210.207929.2395
41.1468-0.0939-0.15231.85510.82241.01420.3158-0.296-0.07570.7565-0.3277-0.32450.3909-0.29020.02060.4456-0.177-0.17140.45420.11050.3825-11.3621.582637.1431
50.3103-0.2603-0.05951.21720.36511.18930.1662-0.1611-0.00760.0857-0.1474-0.7355-0.1564-0.0846-0.03630.2374-0.0112-0.01580.30470.05830.5152-1.2560.541230.9573
60.69171.1822-0.09463.37361.71672.70060.05660.0704-0.3015-0.10720.3121-0.7201-0.20630.3054-0.13740.2885-0.0170.13950.42460.13390.75113.054363.049322.2939
71.67740.1198-0.22581.2246-0.13730.9974-0.06340.1169-0.0606-0.2963-0.0298-0.3269-0.28390.2759-0.24670.664-0.10290.43830.36940.32730.94183.677771.634116.4032
80.75110.1187-0.03082.39960.82961.32550.19950.18490.0624-1.2695-0.391-0.1044-0.642-0.2950.14460.78930.24240.05790.43820.06440.3312-12.839159.77289.4322
90.4235-0.0028-0.20320.91270.37250.79260.2085-0.1676-0.0594-0.2634-0.32370.0260.0081-0.24070.08920.21980.02-0.02730.4752-0.03540.2916-23.974819.36413.9643
101.27350.95841.04721.17530.64131.30090.2841-0.1564-0.0840.1341-0.4570.42220.1431-0.76510.04170.29120.0136-0.00220.6709-0.17060.4841-31.262718.279213.4925
111.60610.1742-0.43292.92061.24452.99930.0579-0.2202-0.2784-0.3184-0.29050.37520.417-0.27320.25180.49810.1092-0.09070.4491-0.08470.3241-27.684212.8005-1.1126
120.88650.5424-0.04912.6080.3950.3790.01990.0395-0.1194-1.4979-0.225-0.1332-0.2622-0.1917-0.08060.6810.14280.04560.3991-0.0170.2674-18.458925.986-3.9026
130.2743-0.13140.25581.12910.23230.6685-0.00450.20720.1206-0.28230.1504-0.2214-0.47240.3035-0.16541.41360.00530.50080.4922-0.00580.4019-4.919134.5689-9.6178
141.66710.40120.60140.40790.05490.96460.27940.35290.002-0.59660.1239-0.4523-0.35880.3230.93150.81550.02910.49120.5509-0.09750.6690.080223.8445-6.4135
152.5344-0.40440.72211.5118-0.41581.8391-0.0085-0.0115-0.2198-0.695-0.19330.0052-0.3147-0.11410.24480.38850.12040.00650.367-0.05210.3485-16.132924.73945.2944
160.65780.07570.07441.30121.19751.1012-0.3461-0.00390.364-1.3746-0.04250.1041-0.6965-0.28210.11811.29760.1694-0.19750.4949-0.05340.3599-22.605333.8886-8.6296
170.84190.4380.10021.20510.2671.36190.09940.4552-0.0289-0.6217-0.0888-0.1269-0.17020.1392-0.09091.58260.16880.22160.63110.00580.4493-16.427720.7905-18.1154
180.76310.17570.25831.26040.20551.15060.15660.1185-0.14850.063-0.61410.24240.0031-0.43960.21960.24250.04740.0290.5899-0.14680.3515-23.905461.647333.3408
191.0426-0.7953-0.53650.73850.26560.41850.1793-0.3925-0.22640.0914-0.58410.54940.0055-0.52520.14960.3386-0.01990.02420.8062-0.3330.5348-31.083962.677734.4214
201.1974-1.00241.60721.1833-1.35312.1516-0.4141-0.030.39460.4271-0.48920.4325-0.4966-0.4918-0.50010.5477-0.14860.17720.6283-0.36250.4193-26.498467.974648.7316
210.718-0.6338-0.05192.86610.63230.7930.1007-0.24050.07311.593-0.4056-0.19840.5124-0.3088-0.17370.7506-0.21530.08350.4603-0.09370.207-17.025455.080450.7873
221.6347-0.027-0.6761.01430.64120.7688-0.14160.0239-0.24210.40530.0448-0.1110.1791-0.0354-0.29581.2346-0.081-0.34260.2382-0.00890.4713-3.215846.606955.4648
231.5175-0.7072-0.07540.99640.46451.24370.0547-0.43370.23080.54510.0279-0.59820.00790.23360.04820.8859-0.1515-0.38490.5247-0.00920.68671.458757.722951.7372
243.3775-0.1357-0.72692.6242-0.87353.1110.1236-0.12170.2710.8154-0.52380.0691-0.0362-0.35810.36940.4198-0.10590.00360.4932-0.06310.2858-15.263956.452241.5004
250.8015-0.0993-0.25060.5364-0.13130.4369-0.2575-0.2938-0.20710.6058-0.05470.10920.2049-0.0269-0.2451.2527-0.34010.25810.6207-0.01130.299-20.848648.648955.279
262.6060.72361.63780.93030.37151.0383-0.13470.0256-0.56240.7836-0.16930.12250.7771-0.4519-0.14071.3313-0.20240.53470.6453-0.17140.6014-20.500343.987356.7019
271.1048-0.7580.26541.14020.19820.79180.0183-0.4176-0.05690.6714-0.0222-0.11130.6687-0.03980.00721.58750.002-0.14040.6426-0.08490.3993-13.52959.882664.7216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )A1 - 63
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 78 )A64 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 108 )A92 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 311 )A109 - 311
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 63 )B1 - 63
6X-RAY DIFFRACTION6chain 'B' and (resid 64 through 79 )B64 - 79
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 108 )B92 - 108
8X-RAY DIFFRACTION8chain 'B' and (resid 109 through 311 )B109 - 311
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 48 )C1 - 48
10X-RAY DIFFRACTION10chain 'C' and (resid 49 through 71 )C49 - 71
11X-RAY DIFFRACTION11chain 'C' and (resid 72 through 108 )C72 - 108
12X-RAY DIFFRACTION12chain 'C' and (resid 109 through 178 )C109 - 178
13X-RAY DIFFRACTION13chain 'C' and (resid 179 through 195 )C179 - 195
14X-RAY DIFFRACTION14chain 'C' and (resid 196 through 216 )C196 - 216
15X-RAY DIFFRACTION15chain 'C' and (resid 217 through 242 )C217 - 242
16X-RAY DIFFRACTION16chain 'C' and (resid 243 through 285 )C243 - 285
17X-RAY DIFFRACTION17chain 'C' and (resid 286 through 311 )C286 - 311
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 48 )D1 - 48
19X-RAY DIFFRACTION19chain 'D' and (resid 49 through 71 )D49 - 71
20X-RAY DIFFRACTION20chain 'D' and (resid 72 through 108 )D72 - 108
21X-RAY DIFFRACTION21chain 'D' and (resid 109 through 178 )D109 - 178
22X-RAY DIFFRACTION22chain 'D' and (resid 179 through 195 )D179 - 195
23X-RAY DIFFRACTION23chain 'D' and (resid 196 through 216 )D196 - 216
24X-RAY DIFFRACTION24chain 'D' and (resid 217 through 242 )D217 - 242
25X-RAY DIFFRACTION25chain 'D' and (resid 243 through 271 )D243 - 271
26X-RAY DIFFRACTION26chain 'D' and (resid 272 through 285 )D272 - 285
27X-RAY DIFFRACTION27chain 'D' and (resid 286 through 311 )D286 - 311

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