[English] 日本語
Yorodumi
- PDB-3c8m: Crystal structure of homoserine dehydrogenase from Thermoplasma v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c8m
TitleCrystal structure of homoserine dehydrogenase from Thermoplasma volcanium
ComponentsHomoserine dehydrogenase
KeywordsOXIDOREDUCTASE / structural genomics / APC89447 / homoserine / dehydrogenase / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / NADP binding
Similarity search - Function
Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Homoserine dehydrogenase lacking ACT domain / Homoserine dehydrogenase, catalytic / Homoserine dehydrogenase / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
homoserine dehydrogenase
Similarity search - Component
Biological speciesThermoplasma volcanium GSS1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Hendricks, R. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of homoserine dehydrogenase from Thermoplasma volcanium.
Authors: Osipiuk, J. / Hendricks, R. / Abdullah, J. / Joachimiak, A.
History
DepositionFeb 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5095
Polymers37,1251
Non-polymers3844
Water6,161342
1
A: Homoserine dehydrogenase
hetero molecules

A: Homoserine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,01910
Polymers74,2502
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.404, 108.404, 60.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21A-481-

HOH

DetailsAUTHORS STATE THAT THE DIMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

-
Components

#1: Protein Homoserine dehydrogenase /


Mass: 37125.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium GSS1 (archaea) / Species: Thermoplasma volcanium / Strain: GSS1 / DSM 4299 / IFO 15438 / JCM 9571 / Gene: TVG0375766, TV0389 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q97BR6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.76 Å3/Da / Density % sol: 55.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Lithium sulfate, 0.12 M Tris buffer, 2 M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2008
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→37.2 Å / Num. all: 32528 / Num. obs: 32528 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.102 / Χ2: 1.332 / Net I/σ(I): 8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 3.47 / Num. unique all: 3209 / Χ2: 1.119 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→37.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.805 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.123 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1640 5.1 %RANDOM
Rwork0.156 ---
all0.157 32410 --
obs0.157 32410 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 20 342 2912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222793
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9823805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79324.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58915520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5361523
X-RAY DIFFRACTIONr_chiral_restr0.1120.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022118
X-RAY DIFFRACTIONr_nbd_refined0.2090.21302
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.230
X-RAY DIFFRACTIONr_mcbond_it0.9971.51743
X-RAY DIFFRACTIONr_mcangle_it1.5822747
X-RAY DIFFRACTIONr_scbond_it2.631185
X-RAY DIFFRACTIONr_scangle_it3.8844.51033
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 125 -
Rwork0.187 2220 -
all-2345 -
obs-2345 98.9 %
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)
12.66860.04810.71942.15532.05522.12970.00140.2462-0.0144-0.21620.0063-0.1149-0.15130.1077-0.00770.0092-0.00070.02420.06670.00260.076749.717645.4226-2.4085
22.3287-0.78051.3311.0989-0.7451.7564-0.03230.0656-0.0103-0.06110.0162-0.0924-0.03360.07310.01610.0055-0.00690.0240.07130.030.069954.999847.5196-0.4174
32.62861.3331-0.08585.3282-1.72320.64320.05050.2396-0.2293-0.1216-0.0482-0.50990.03120.1049-0.00230.00210.02410.0330.0766-0.02410.126159.363839.0707-3.2405
46.9568-0.6242-0.27890.2351-1.18798.2241-0.21150.1726-0.51130.1055-0.0535-0.18070.90140.38980.2650.0345-0.0050.03450.11030.020.184163.956844.97037.0263
50.94220.2148-0.75450.3109-0.13661.07320.0056-0.13520.0621-0.02120.0213-0.0271-0.02620.0328-0.02680.02710.0046-0.0130.07960.00240.080547.307949.164415.5391
60.82610.17920.15680.03890.0340.02980.013-0.04830.0858-0.0088-0.0445-0.0209-0.0415-0.08690.03140.05310.0191-0.00290.06720.00210.076335.976252.67259.523
71.5072-1.39310.06492.132-0.02320.9634-0.0355-0.1429-0.0258-0.0221-0.00560.07150.0286-0.09350.04110.04790.00230.01750.07190.01270.055426.317130.118313.2988
88.3864-4.2091-5.024510.962-7.925115.343-0.0506-0.39840.28071.0532-0.0166-0.6679-0.6310.98270.06720.18760.0326-0.02330.0953-0.00140.032939.784518.68311.8656
90.23680.65330.01532.30490.63511.2454-0.0227-0.078-0.02280.13750.0543-0.20650.08980.0238-0.03160.03820.02410.00680.09920.01450.03532.875538.383220.9554
109.5327-2.745110.4633.6414-1.255312.5677-0.4395-0.1367-1.56260.42840.80660.2847-0.0251-0.2493-0.36710.1646-0.01110.09520.10330.18550.124325.224720.110921.3659
110.98050.0064-0.03465.89232.63131.47280.0153-0.22550.0243-0.106-0.0031-0.0671-0.0672-0.3225-0.01220.03490.03450.0130.11590.01020.02421.873239.482418.9982
121.48990.45880.04290.80960.11324.5222-0.0412-0.0433-0.01280.0012-0.05790.060.0963-0.56420.099-0.0064-0.01040.01480.1027-0.00760.070919.040231.384812.1261
131.4247-1.0167-0.37521.73020.41760.1212-0.0326-0.0963-0.0473-0.02990.0695-0.0110.02050-0.03690.05190.02550.00580.080900.049323.702439.56324.6599
143.42630.72-0.33358.13821.6971.38420.05980.2150.0834-0.0266-0.07290.106-0.11390.04650.01310.01620.0243-0.00130.0880.010.050940.801845.96650.5669
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 274 - 30
2X-RAY DIFFRACTION2AA28 - 5031 - 53
3X-RAY DIFFRACTION3AA51 - 6554 - 68
4X-RAY DIFFRACTION4AA66 - 8169 - 84
5X-RAY DIFFRACTION5AA82 - 13085 - 133
6X-RAY DIFFRACTION6AA131 - 163134 - 166
7X-RAY DIFFRACTION7AA164 - 190167 - 193
8X-RAY DIFFRACTION8AA191 - 204194 - 207
9X-RAY DIFFRACTION9AA205 - 241208 - 244
10X-RAY DIFFRACTION10AA242 - 250245 - 253
11X-RAY DIFFRACTION11AA251 - 267254 - 270
12X-RAY DIFFRACTION12AA268 - 283271 - 286
13X-RAY DIFFRACTION13AA284 - 307287 - 310
14X-RAY DIFFRACTION14AA308 - 325311 - 328

+
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