[English] 日本語
Yorodumi
- PDB-3zr4: STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zr4
TitleSTRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX
Components
  • IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF
  • IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
KeywordsTRANSFERASE
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / L-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
GLUTAMINE / 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: 2.41 Å
AuthorsVega, M.C. / Kuper, J. / Haeger, M.C. / Mohrlueder, J. / Marquardt, S. / Sterner, R. / Wilmanns, M.
Citation
Journal: 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.
#1: Journal: Structure / Year: 2002
Title: Structural Evidence for Ammonia Tunneling Across the (Beta Alpha)(8) Barrel of the Imidazole Glycerol Phosphate Synthase Bienzyme Complex.
Authors: Douangamath, A. / Walker, M. / Beismann-Driemeyer, S. / Vega-Fernandez, M.C. / Sterner, R. / Wilmanns, M.
History
DepositionJun 13, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 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_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)153,59015
Polymers152,6536
Non-polymers9379
Water3,675204
1
A: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF
B: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3076
Polymers50,8842
Non-polymers4224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-4 kcal/mol
Surface area18370 Å2
MethodPISA
2
C: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF
D: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2155
Polymers50,8842
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-7.3 kcal/mol
Surface area18520 Å2
MethodPISA
3
E: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISF
F: IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0694
Polymers50,8842
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-8.3 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.399, 85.399, 171.109
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.5041, 0.8637, -0.0011), (0.8636, 0.5041, 0.0053), (0.0051, 0.0018, -1)0.1867, -0.1986, -0.0678
2given(0.9616, 0.2741, 0.0167), (-0.2745, 0.9607, 0.0419), (-0.0045, -0.0448, 0.999)42.6785, 24.3011, -7.3212
3given(-0.4984, 0.867, 0.0012), (0.8669, 0.4984, 0.0051), (0.0038, 0.0036, -1)-0.0669, 0.1203, -0.1828
4given(0.9458, 0.3237, -0.0249), (-0.3228, 0.9459, 0.0333), (0.0343, -0.0234, 0.9991)43.2999, 24.7004, -7.5492

-
Components

#1: Protein IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE SUBUNIT 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: RBSIISPHI-TMHISF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3310 / Variant (production host): DELTA-TRPEA2
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 / IGPS SUBUNIT HISH / TMHISH


Mass: 23130.564 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: RBSIISPHI-TMHISH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3310 / Variant (production host): DELTA-TRPEA2
References: UniProt: Q9X0C8, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.507
11-H-K, K, -L20.493
ReflectionResolution: 2.4→55.95 Å / Num. obs: 51685 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 88.9

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GPW

1gpw


Resolution: 2.41→55.96 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.587 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25771 4271 8.3 %RANDOM
Rwork0.19357 ---
obs0.19897 47409 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.957 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å20 Å20 Å2
2--3.99 Å20 Å2
3----7.98 Å2
Refinement stepCycle: LAST / Resolution: 2.41→55.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10462 0 62 204 10728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02210692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.97714384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2251321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55423.422488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.208151942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5841590
X-RAY DIFFRACTIONr_chiral_restr0.0930.21613
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217961
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4761.56569
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.881210579
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.534123
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3214.53805
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.411→2.474 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 257 -
Rwork0.283 3150 -
obs--86.45 %
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)
11.57570.16310.11031.09490.41661.72160.1458-0.0072-0.13930.0498-0.1603-0.21820.18040.29850.01450.03060.0301-0.00810.1090.03630.156450.114226.7176-7.0285
22.1734-0.55070.15151.6364-0.21671.33470.0109-0.20480.04760.25050.01330.0264-0.0568-0.0226-0.02420.0969-0.05110.00580.058-0.01480.070633.562734.386714.9227
30.9010.0633-0.49541.4088-0.12851.786-0.0617-0.08050.0974-0.14490.07840.2672-0.1474-0.3125-0.01680.07160.035-0.03580.0955-0.00350.1773-2.153656.66847.0248
42.2811-0.55760.21251.780.33641.52670.02230.22340.0036-0.19810.0043-0.0077-0.03230.118-0.02660.1229-0.04670.01170.04910.00580.070712.949746.3948-14.9727
51.05520.12170.42981.03390.38242.257300.0115-0.0327-0.0826-0.0306-0.06310.15760.03520.03060.1396-0.02650.02720.1017-0.01980.25616.80754.210.5626
61.6395-0.362-0.00441.2845-0.2251.0169-0.078-0.1264-0.00790.05850.09660.18830.0291-0.2505-0.01860.14090.0012-0.00610.0948-0.02890.2367-11.41065.417723.2426
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 253
2X-RAY DIFFRACTION2B1 - 200
3X-RAY DIFFRACTION2B1205
4X-RAY DIFFRACTION3C1 - 253
5X-RAY DIFFRACTION4D1 - 200
6X-RAY DIFFRACTION4B - D1205
7X-RAY DIFFRACTION5E1 - 253
8X-RAY DIFFRACTION6F1 - 200

+
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