[English] 日本語
Yorodumi
- PDB-6ka0: Silver-bound E.coli Malate dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
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 / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / 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 / (S)-malate dehydrogenase (NAD+, oxaloacetate-forming) / 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 / cytoplasm / cytosol
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: Chem Sci / Year: 2025
Title: Unprecedented allosteric inhibition of E. coli malate dehydrogenase by silver(i) from atomic resolution analysis.
Authors: Wang, H. / Wang, M. / Yang, X. / Yan, A. / Hao, Q. / Li, H. / 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
Revision 1.2Mar 18, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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, (S)-malate dehydrogenase (NAD+, oxaloacetate-forming)
#2: Chemical
ChemComp-AG / SILVER ION


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more