[English] 日本語
Yorodumi
- PDB-4xxv: Crystal structure of 3-isopropylmalate dehydrogenase from Burkhol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xxv
TitleCrystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / 3-isopropylmalate dehydrogenase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Isopropylmalate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4795
Polymers78,6322
Non-polymers8483
Water17,366964
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-36 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.350, 60.900, 105.050
Angle α, β, γ (deg.)90.000, 117.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

21B-580-

HOH

Detailsbiological unit is a dimer

-
Components

#1: Protein 3-isopropylmalate dehydrogenase / / 3-IPM-DH / Beta-IPM dehydrogenase / IMDH


Mass: 39315.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: leuB, BTH_II0674 / Plasmid: ButhA.00092.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2T7H6, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 964 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytics MCSG1 B7: 25.5% PEG 4000, 15% glycerol, 170mM Ammonium acetate; ButhA.00092.a.B1.PS0xxxx at 12.64 mg/ml; the drop was overlayed with 5ul 5mM NAD in reservoir and soaked over ...Details: Microlytics MCSG1 B7: 25.5% PEG 4000, 15% glycerol, 170mM Ammonium acetate; ButhA.00092.a.B1.PS0xxxx at 12.64 mg/ml; the drop was overlayed with 5ul 5mM NAD in reservoir and soaked over night; cryo: direct; tray 257491b7, puck tiz0-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 15, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 86107 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 13.32 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.981 / Net I/σ(I): 30.23 / Num. measured all: 614892
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.7-1.743.40.910.2864.1818874652955900.33685.6
1.74-1.790.9560.2595.4726836640057760.2990.2
1.79-1.840.970.2226.2727080617657130.24792.5
1.84-1.90.9760.27.0227428605557110.22394.3
1.9-1.960.9840.13410.8427712581956240.14996.6
1.96-2.030.990.12111.8827929564955560.13598.4
2.03-2.110.9930.09815.3228363546054340.10999.5
2.11-2.190.9960.08420.2233362524952290.09199.6
2.19-2.290.9970.07126.9935622505450410.07799.7
2.29-2.40.9980.06428.8236167482347810.06999.1
2.4-2.530.9990.05434.3537295461346040.05899.8
2.53-2.690.9990.0538.5638245432343140.05499.8
2.69-2.870.9990.04547.4942984411941120.04799.8
2.87-3.110.0453.1142378379137860.04299.9
3.1-3.410.03263.3839702354235340.03499.8
3.4-3.810.02973.8835276318631750.03199.7
3.8-4.3910.02586.2431345283428170.02699.4
4.39-5.3810.02389.8326547238723810.02499.7
5.38-7.610.02876.2920808188318750.02999.6
7.610.02197.5210939107510540.02298

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure, 4iwh

4iwh


Resolution: 1.7→43.612 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1738 2000 2.32 %Random selection
Rwork0.149 84097 --
obs0.1495 86097 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.38 Å2 / Biso mean: 15.7571 Å2 / Biso min: 4.49 Å2
Refinement stepCycle: final / Resolution: 1.7→43.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 62 975 6393
Biso mean--13.76 28.13 -
Num. residues----711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115615
X-RAY DIFFRACTIONf_angle_d1.3257642
X-RAY DIFFRACTIONf_chiral_restr0.067858
X-RAY DIFFRACTIONf_plane_restr0.0061009
X-RAY DIFFRACTIONf_dihedral_angle_d13.2822099
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.24281250.1915268539386
1.7425-1.78960.24081320.17565556568890
1.7896-1.84230.1881350.17225685582092
1.8423-1.90180.23541390.17455837597694
1.9018-1.96970.1781420.16735970611297
1.9697-2.04860.17231450.15146081622699
2.0486-2.14180.16441460.148861506296100
2.1418-2.25470.18511480.149561966344100
2.2547-2.3960.17171460.15236140628699
2.396-2.5810.18451460.145761806326100
2.581-2.84070.19671480.151761946342100
2.8407-3.25160.16411480.151262366384100
3.2516-4.09620.16451480.134362396387100
4.0962-43.62610.1321520.131163656517100
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)
10.98510.06440.33622.00350.08441.30550.02720.03250.0786-0.0639-0.0674-0.177-0.14620.18310.00380.0586-0.02810.00690.10410.02280.087510.1915.948437.0658
20.70040.06420.10770.9649-0.10360.5350.03280.0612-0.00490.0347-0.0431-0.0908-0.02740.05020.00940.0588-0.00150.00020.06440.00930.0559-10.95724.718719.5129
30.6575-0.42320.31262.02-0.41070.99950.11630.0792-0.1127-0.2087-0.0910.08510.17140.1617-0.01360.08310.0266-0.01220.0821-0.01050.09395.8591-9.105230.2582
40.67970.07960.27731.9826-0.11120.93250.02060.03640.0481-0.0592-0.02510.27280.0034-0.2389-0.02660.04320.0118-0.00940.1152-0.00490.0883-43.24471.42287.479
52.54410.7093-0.13311.5885-0.4341.292-0.06320.1360.1699-0.04140.01130.0634-0.1406-0.08510.05130.0710.0296-0.01080.08350.0030.075-35.331410.133810.1177
60.9923-0.45090.05372.0318-0.01980.64040.0325-0.1071-0.17550.0406-0.01920.06360.0784-0.0762-0.00290.0871-0.0108-0.00480.07760.00140.0665-30.7844-9.613226.0431
70.9310.2549-0.20180.8901-0.20210.62670.0592-0.11550.07640.087-0.05080.0197-0.1199-0.0116-0.00580.0889-0.0010.00420.0818-0.01920.0556-25.92510.157932.1106
80.37110.42970.51870.85920.13661.21190.0423-0.0345-0.04180.0346-0.0037-0.02540.0515-0.0381-0.0460.05530.00640.00990.0665-0.0010.0659-31.1269-2.256621.4644
91.4866-0.8687-0.53161.52540.7980.4866-0.0888-0.2073-0.09060.52470.01290.33050.3144-0.23140.02520.1722-0.05620.04810.16990.00620.1149-45.4482-10.303921.3832
102.1399-1.049-0.18061.9051-0.42341.36690.0838-0.0148-0.41540.1524-0.0477-0.04220.3228-0.13190.01470.1469-0.0364-0.01790.0751-0.00330.1369-36.3354-19.846412.0714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 92 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 93 through 256 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 257 through 355 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 50 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 92 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 93 through 122 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 123 through 230 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 231 through 293 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 294 through 327 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 328 through 355 )B0

+
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