[English] 日本語
Yorodumi
- PDB-4hyr: Structure of putative Glucarate dehydratase from Acidaminococcus ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hyr
TitleStructure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder
ComponentsGlucarate dehydratase
KeywordsLYASE / Glucarate dehydratase / New York Structural Genomics Research Consortium / NYSGRC / Protein Structure Initiative / PSI-Biology
Function / homology
Function and homology information


D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily ...D-Glucarate dehydratase-like / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative glucarate dehydratase
Similarity search - Component
Biological speciesAcidaminococcus sp. D21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.84 Å
AuthorsHegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be published
Title: Structure of putative Glucarate dehydratase from Acidaminococcus sp. D21 with unusual static disorder
Authors: Hegde, R.P. / Toro, R. / Burley, S.K. / Almo, S.C. / Ramagopal, U.A. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,04410
Polymers102,5682
Non-polymers4778
Water9,512528
1
A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules

A: Glucarate dehydratase
B: Glucarate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,08920
Polymers205,1354
Non-polymers95416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-30 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.916, 88.916, 236.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-776-

HOH

21B-715-

HOH

-
Components

#1: Protein Glucarate dehydratase


Mass: 51283.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidaminococcus sp. D21 (bacteria) / Gene: ACDG_00756 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0WBB5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 82827 / Num. obs: 82827 / % possible obs: 99.5 % / Redundancy: 23.8 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.079 / Χ2: 1.378 / Net I/σ(I): 37.238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.84-1.8722.40.973.87537000.8951.21990.2
1.87-1.9124.40.81340831.218100
1.91-1.9424.50.71541111.237100
1.94-1.9824.50.59140681.242100
1.98-2.0324.50.49240981.272100
2.03-2.0724.40.40841231.253100
2.07-2.1224.50.33640761.274100
2.12-2.1824.40.28541131.326100
2.18-2.2524.40.24841081.336100
2.25-2.3224.40.22141181.384100
2.32-2.424.40.1941401.334100
2.4-2.524.30.1741121.377100
2.5-2.6124.30.14241551.409100
2.61-2.7524.20.12441481.4100
2.75-2.9224.10.10841711.463100
2.92-3.1523.80.09241981.413100
3.15-3.4623.30.08241911.342100
3.46-3.9622.60.0742411.377100
3.96-4.9921.70.05843021.649100
4.99-5020.40.05945712.08799.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
HKL2Mapphasing
PHENIXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.84→43.69 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1964 / WRfactor Rwork: 0.1583 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8879 / SU B: 4.97 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1276 / SU Rfree: 0.1201 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 4129 5 %RANDOM
Rwork0.1629 ---
obs0.1647 82357 99.47 %-
all-82357 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.73 Å2 / Biso mean: 26.0755 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0 Å2
2---0.06 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.84→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 27 528 7379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197695
X-RAY DIFFRACTIONr_bond_other_d00.027263
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.97110462
X-RAY DIFFRACTIONr_angle_other_deg0.695316773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3623.923362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.359151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4551555
X-RAY DIFFRACTIONr_chiral_restr0.0850.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0218873
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021768
LS refinement shellResolution: 1.842→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 275 -
Rwork0.226 5625 -
all-5900 -
obs--98.32 %
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)
10.4105-0.10530.3890.4391-0.39040.75680.06970.0312-0.005-0.0562-0.020.06820.1340.0384-0.04970.18570.0089-0.03110.1923-0.02040.1214-0.159337.878857.535
20.40970.0310.18130.1973-0.06730.2225-0.0727-0.030.1259-0.01270.01380.00350.0054-0.04520.0590.15260.0141-0.03250.1739-0.01350.1781-1.760356.959655.8437
30.9428-0.08870.05680.3765-0.21190.2301-0.0755-0.14290.03820.1887-0.0007-0.0406-0.1307-0.10.07620.21270.0058-0.04920.2221-0.04060.076617.490846.257192.9418
40.1790.0999-0.00590.3884-0.14280.16710.0198-0.0306-0.00450.0363-0.073-0.15440.0107-0.02280.05320.16370.0057-0.03940.18120.02380.188133.495442.25480.5846
50.34960.13191.42350.9736-1.970712.60620.082-0.1943-0.25370.6779-0.2136-0.5293-1.359-0.44450.13150.4721-0.1414-0.370.12570.2010.387644.636455.077693.201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2A104 - 442
3X-RAY DIFFRACTION3B1 - 89
4X-RAY DIFFRACTION4B101 - 412
5X-RAY DIFFRACTION5B413 - 442

+
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://pdbjlvh1.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