[English] 日本語
Yorodumi
- PDB-2wjz: Crystal structure of (HisH) K181A Y138A mutant of imidazoleglycer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wjz
TitleCrystal structure of (HisH) K181A Y138A mutant of imidazoleglycerolphosphate synthase (HisH HisF) which displays constitutive glutaminase activity
Components
  • IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
  • IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
KeywordsLYASE/TRANSFERASE / LYASE-TRANSFERASE COMPLEX / AMINO-ACID BIOSYNTHESIS / AMMONIA CHANNEL / HISTIDINE BIOSYNTHESIS / CYCLASE / GLUTAMINASE
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like ...Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Imidazole glycerol phosphate synthase subunit HisF / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsVega, M.C. / List, F. / Razeto, A. / Haeger, M.C. / Babinger, K. / Kuper, J. / Sterner, R. / Wilmanns, M.
CitationJournal: Chem.Biol. / Year: 2012
Title: Catalysis Uncoupling in a Glutamine Amidotransferase Bienzyme by Unblocking the Glutaminase Active Site.
Authors: List, F. / Vega, M.C. / Razeto, A. / Hager, M.C. / Sterner, R. / Wilmanns, M.
History
DepositionJun 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 11-STRANDED BARREL THIS IS REPRESENTED BY A 12-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
B: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
C: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
D: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
E: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
F: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,4889
Polymers152,2036
Non-polymers2853
Water3,765209
1
A: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
B: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8293
Polymers50,7342
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-15.9 kcal/mol
Surface area18250 Å2
MethodPISA
2
E: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
F: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8293
Polymers50,7342
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-13.7 kcal/mol
Surface area17490 Å2
MethodPISA
3
C: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF
D: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8293
Polymers50,7342
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-15.9 kcal/mol
Surface area18110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.935, 93.935, 166.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
12
22
32

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN C AND (RESSEQ 3:11 )OR RESSEQ 36:131 OR RESSEQ 137:144 OR RESSEQ 147:223 OR RESSEQ 234:250 )
211CHAIN A AND (RESSEQ 3:11 OR RESSEQ 36:131 OR RESSEQ 137:144 OR RESSEQ 147:223 OR RESSEQ 234:250 )
311CHAIN E AND (RESSEQ 3:11 OR RESSEQ 36:131 OR RESSEQ 137:144 OR RESSEQ 147:223 OR RESSEQ 234:250 )
112CHAIN D AND (RESSEQ 1:27 OR RESSEQ 44:97 OR RESSEQ 100:198 )
212CHAIN B AND (RESSEQ 1:27 OR RESSEQ 44:97 OR RESSEQ 100:198 )
312CHAIN F AND (RESSEQ 1:27 OR RESSEQ 44:97 OR RESSEQ 100:198 )

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.557714, -0.830033, 0.000841), (-0.82655, 0.555281, -0.092074), (0.075957, -0.052046, -0.995752)-5.89018, -55.3143, -37.3271
2given(-0.557714, -0.830033, 0.000841), (-0.82655, 0.555281, -0.092074), (0.075958, -0.052046, -0.995752)-5.89018, -55.3143, -37.3271
3given(-0.533127, 0.841313, 0.089261), (-0.789393, -0.532613, 0.305257), (0.304358, 0.092279, 0.948077)-5.16571, -38.9182, 33.9183
4given(-0.57489, -0.8181, 0.014554), (-0.80915, 0.565778, -0.158658), (0.121564, -0.102987, -0.987226)-6.72704, -55.8181, -33.982
5given(-0.597672, 0.801676, -0.01024), (-0.758994, -0.561644, 0.329369), (0.258295, 0.204627, 0.944146)-14.0346, -36.6844, 33.1369

-
Components

#1: Protein IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE HISF / IGP SYNTHASE CYCLASE SUBUNIT / IGP SYNTHASE SUBUNIT HISF / IMGP SYNTHASE SUBUNIT HISF / IGPS SUBUNIT HISF


Mass: 27753.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PET11C-HISF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9X0C6, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Protein IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH / IGP SYNTHASE GLUTAMINE AMIDOTRANSFERASE SUBUNIT / IGP SYNTHASE SUBUNIT HISH / IMGP SYNTHASE SUBUNIT ...IGP SYNTHASE GLUTAMINE AMIDOTRANSFERASE SUBUNIT / IGP SYNTHASE SUBUNIT HISH / IMGP SYNTHASE SUBUNIT HISH / TMHISH / IGPS SUBUNIT HISH / AMIDOTRANSFERASE HISH


Mass: 22980.367 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: PDS/RBSII / Production host: ESCHERICHIA COLI K-12 (bacteria) / Strain (production host): W3110
References: UniProt: Q9X0C8, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, LYS 181 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 138 TO ALA ...ENGINEERED RESIDUE IN CHAIN B, LYS 181 TO ALA ENGINEERED RESIDUE IN CHAIN B, TYR 138 TO ALA ENGINEERED RESIDUE IN CHAIN D, LYS 181 TO ALA ENGINEERED RESIDUE IN CHAIN D, TYR 138 TO ALA ENGINEERED RESIDUE IN CHAIN F, LYS 181 TO ALA ENGINEERED RESIDUE IN CHAIN F, TYR 138 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growpH: 8.5
Details: PEG8K 10-12%, 100 MM HEPES PH = 8.5 22.5MM NH4NO3 / NH4AC 5% (V/V) MPD 10 MM DTT 20 MM L-GLN PROT. CONC.= 12 MG/ML

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 12, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.125
ReflectionResolution: 2.6→81.35 Å / Num. obs: 50263 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 65.12 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.43 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPW

1gpw


Resolution: 2.601→39.511 Å / σ(F): 1.97 / Phase error: 28.8 / Stereochemistry target values: TWIN_LSQ_F
Details: RESIDUES 252-253 IN CHAINS C, A, E AND 199-201 IN CHAINS D, B, F ARE MISSING BECAUSE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2184 2559 5.09 %
Rwork0.1852 --
obs0.1869 50262 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.229 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 76 Å2
Baniso -1Baniso -2Baniso -3
1--12.7015 Å20 Å20 Å2
2---12.7015 Å20 Å2
3----15.0461 Å2
Refinement stepCycle: LAST / Resolution: 2.601→39.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9979 0 15 209 10203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610579
X-RAY DIFFRACTIONf_angle_d0.99314245
X-RAY DIFFRACTIONf_dihedral_angle_d17.7473917
X-RAY DIFFRACTIONf_chiral_restr0.0631607
X-RAY DIFFRACTIONf_plane_restr0.0061835
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1582X-RAY DIFFRACTIONPOSITIONAL
12A1582X-RAY DIFFRACTIONPOSITIONAL0.045
13E1560X-RAY DIFFRACTIONPOSITIONAL0.04
21D1432X-RAY DIFFRACTIONPOSITIONAL
22B1432X-RAY DIFFRACTIONPOSITIONAL0.08
23F1445X-RAY DIFFRACTIONPOSITIONAL0.098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.64590.34831430.30652378X-RAY DIFFRACTION98
2.6459-2.6940.35161180.28952408X-RAY DIFFRACTION98
2.694-2.74580.31991470.27932350X-RAY DIFFRACTION98
2.7458-2.80180.29861310.26662369X-RAY DIFFRACTION98
2.8018-2.86270.28621270.26522397X-RAY DIFFRACTION98
2.8627-2.92930.33321150.25542430X-RAY DIFFRACTION98
2.9293-3.00250.27781250.24452345X-RAY DIFFRACTION98
3.0025-3.08370.2471410.24432394X-RAY DIFFRACTION98
3.0837-3.17440.26611280.23562401X-RAY DIFFRACTION98
3.1744-3.27680.28741340.22362389X-RAY DIFFRACTION98
3.2768-3.39380.2481340.21722352X-RAY DIFFRACTION98
3.3938-3.52970.23441230.20082402X-RAY DIFFRACTION98
3.5297-3.69020.2141180.18862411X-RAY DIFFRACTION98
3.6902-3.88460.19791240.17332412X-RAY DIFFRACTION98
3.8846-4.12770.20821350.16072350X-RAY DIFFRACTION98
4.1277-4.4460.16761160.13932402X-RAY DIFFRACTION98
4.446-4.89270.14071210.13042414X-RAY DIFFRACTION98
4.8927-5.5990.18731340.14762352X-RAY DIFFRACTION98
5.599-7.04760.23371150.17592390X-RAY DIFFRACTION98
7.0476-39.51530.17091280.14882359X-RAY DIFFRACTION98
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)
11.71490.49230.83851.2505-0.05141.5033-0.36850.3023-0.1721-0.09730.2282-0.2933-0.01820.23180.10510.3156-0.09030.10850.2836-0.08260.3518-46.177822.6145-20.4314
21.43140.25540.09120.8640.31521.57680.0491-0.05960.05740.0350.0160.19540.0417-0.2259-0.0590.2961-0.05720.03290.30230.04450.31610.9868-2.9852-21.3957
32.0203-0.06630.26821.70370.54121.8929-0.2072-0.06210.11720.02160.2748-0.24080.03390.1678-0.04010.35970.0618-0.05950.3397-0.12880.2547-48.1162-18.2515-40.9287
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR CHAIN B
2X-RAY DIFFRACTION2CHAIN C OR CHAIN D
3X-RAY DIFFRACTION3CHAIN E OR CHAIN F

+
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