[English] 日本語
Yorodumi
- PDB-6cmz: 2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Deh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cmz
Title2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD
ComponentsDihydrolipoyl dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase (NADH) activity / flavin adenine dinucleotide binding
Similarity search - Function
Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Dihydrolipoamide dehydrogenase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Dihydrolipoyl dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionMar 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.3Feb 11, 2026Group: Database references / Category: citation / citation_author
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,36717
Polymers195,8334
Non-polymers6,53413
Water6,485360
1
A: Dihydrolipoyl dehydrogenase
B: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8569
Polymers97,9172
Non-polymers3,9397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-90 kcal/mol
Surface area36560 Å2
MethodPISA
2
C: Dihydrolipoyl dehydrogenase
D: Dihydrolipoyl dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5128
Polymers97,9172
Non-polymers2,5956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-77 kcal/mol
Surface area36100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.565, 107.246, 105.427
Angle α, β, γ (deg.)90.00, 106.09, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydrolipoyl dehydrogenase


Mass: 48958.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: lpdV, BCAL1215 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: B4EEF2, dihydrolipoyl dehydrogenase

-
Non-polymers , 7 types, 373 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: Protein: 8.0 mg/ml, 0.5 Sodium chloride, 0.01M Tris pH 8.3, 1mM FAD; Screen: PACT (D1), 0.1M MMT buffer pH 4.0, 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2018 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 79190 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 42.9 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.059 / Rrim(I) all: 0.124 / Rsym value: 0.109 / Χ2: 1.004 / Net I/σ(I): 13.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3954 / CC1/2: 0.624 / Rpim(I) all: 0.443 / Rrim(I) all: 0.909 / Rsym value: 0.791 / Χ2: 1.003 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LVL

1lvl


Resolution: 2.3→29.21 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 19.452 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.423 / ESU R Free: 0.26 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 3962 5 %RANDOM
Rwork0.19868 ---
obs0.20144 75207 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.659 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å21.03 Å2
2--0.44 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13576 0 432 360 14368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914342
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213715
X-RAY DIFFRACTIONr_angle_refined_deg1.4662.00119549
X-RAY DIFFRACTIONr_angle_other_deg0.891331486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.07751852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.93522.196551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.891152223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.45915148
X-RAY DIFFRACTIONr_chiral_restr0.0820.22249
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.02116027
X-RAY DIFFRACTIONr_gen_planes_other0.0190.022930
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4583.1697399
X-RAY DIFFRACTIONr_mcbond_other1.4583.1687398
X-RAY DIFFRACTIONr_mcangle_it2.434.7489254
X-RAY DIFFRACTIONr_mcangle_other2.434.7489255
X-RAY DIFFRACTIONr_scbond_it1.8553.6816943
X-RAY DIFFRACTIONr_scbond_other1.8553.6826944
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0315.42810296
X-RAY DIFFRACTIONr_long_range_B_refined5.38938.9316023
X-RAY DIFFRACTIONr_long_range_B_other5.3738.85115975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 256 -
Rwork0.276 5395 -
obs--97.7 %
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)
12.58360.56860.86151.75111.2335.5691-0.0006-0.23550.27730.323-0.1429-0.0229-0.22580.17290.14350.2422-0.0914-0.0420.1273-0.05560.071911.345520.873744.4139
21.18260.1937-0.02941.1702-0.01281.45770.02080.20550.0803-0.1005-0.1024-0.2737-0.0740.2360.08160.0291-0.01070.02730.11890.05670.083414.05349.53919.6892
34.64010.8836-0.49462.75380.10173.83740.0752-0.2439-0.18210.3796-0.1856-0.33170.17790.40620.11040.0994-0.0388-0.06260.09940.05660.057517.25857.892943.978
41.3711-0.0168-0.14291.3224-0.48152.60490.07080.0757-0.13660.068-0.0675-0.0489-0.01290.2117-0.00330.07510.00690.00560.0446-0.04040.07350.1845-9.887929.356
51.0965-0.7734-0.04281.6014-1.40492.17110.09580.0643-0.275-0.104-0.05420.3180.04630.0084-0.04150.12790.0073-0.0080.0771-0.03980.1604-8.6742-11.438630.3595
60.58060.60370.05672.3775-0.7170.76610.00680.2044-0.2026-0.16710.090.15690.1967-0.0153-0.09680.27250.0437-0.04360.194-0.03570.2627-22.6599-11.521815.8258
71.8990.2358-0.15592.0062-0.57511.32870.0330.3580.2061-0.1650.17150.53360.0411-0.2392-0.20450.04630.0387-0.07330.16530.03840.1988-30.61650.302912.8488
83.9081-0.7536-0.05972.8427-0.23923.01590.0323-0.0024-0.16610.30990.02450.56310.2017-0.3053-0.05680.0555-0.02130.05420.03230.01890.2326-34.3946-16.011130.4748
91.4189-0.07660.02751.2743-0.21851.99170.0202-0.09280.0540.14830.02410.2031-0.0969-0.075-0.04430.1330.01120.03390.041-0.03620.0901-13.71385.319435.6984
101.39630.6499-2.08072.0659-0.23163.4322-0.1285-0.1334-0.1220.1139-0.08280.07760.3380.18430.21130.2314-0.0435-0.07390.12320.10480.2304-34.642128.613641.9892
111.92630.5517-0.67450.912-0.26951.2402-0.10020.4093-0.2106-0.27990.06720.13260.2405-0.31230.0330.1646-0.0529-0.09140.1468-0.02650.1099-34.563738.563517.8265
121.36380.4503-0.61651.72660.47192.23490.1256-0.10360.03230.1042-0.09540.3040.0665-0.3033-0.03030.092-0.024-0.03520.12170.0530.1303-38.571742.378339.6901
131.8604-0.61790.01462.46470.22751.7261-0.0482-0.00430.3217-0.06260.04720.0168-0.0269-0.01490.0010.16470.0249-0.01270.03450.02220.0767-17.8460.918628.7408
143.4106-1.03930.08722.42161.89413.00740.05720.15950.4271-0.6256-0.0141-0.563-0.27960.0459-0.04310.34230.03630.1520.03970.03090.34817.496973.714323.1396
150.89130.1061-0.17841.64790.61030.9594-0.00580.13140.0631-0.47080.0738-0.4473-0.0507-0.0041-0.0680.23250.02380.1240.09750.03690.22945.495750.689915.5979
161.2836-0.3986-0.33933.91891.42221.8323-0.0019-0.1178-0.00530.29420.063-0.82530.15280.1758-0.06110.06040.02530.00090.03440.04370.331113.484652.626927.0365
171.7071-0.8126-0.03742.60170.42062.8991-0.1154-0.1487-0.12270.00170.1585-0.02020.0965-0.0008-0.04310.12940.02880.0120.07180.03820.0295-9.775742.659737.1007
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 38
2X-RAY DIFFRACTION2A39 - 271
3X-RAY DIFFRACTION3A272 - 336
4X-RAY DIFFRACTION4A337 - 412
5X-RAY DIFFRACTION5A413 - 463
6X-RAY DIFFRACTION6B2 - 75
7X-RAY DIFFRACTION7B76 - 279
8X-RAY DIFFRACTION8B280 - 336
9X-RAY DIFFRACTION9B337 - 460
10X-RAY DIFFRACTION10C1 - 44
11X-RAY DIFFRACTION11C45 - 270
12X-RAY DIFFRACTION12C271 - 352
13X-RAY DIFFRACTION13C353 - 463
14X-RAY DIFFRACTION14D2 - 38
15X-RAY DIFFRACTION15D39 - 227
16X-RAY DIFFRACTION16D228 - 343
17X-RAY DIFFRACTION17D344 - 460

+
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