[English] 日本語
Yorodumi
- PDB-3euc: Crystal structure of histidinol-phosphate aminotransferase (YP_29... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3euc
TitleCrystal structure of histidinol-phosphate aminotransferase (YP_297314.1) from RALSTONIA EUTROPHA JMP134 at 2.05 A resolution
ComponentsHistidinol-phosphate aminotransferase 2
KeywordsTRANSFERASE / YP_297314.1 / histidinol-phosphate aminotransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Amino-acid biosynthesis / Aminotransferase / Histidine biosynthesis / Pyridoxal phosphate / Aminotransferase class I and II
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Histidinol-phosphate aminotransferase family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...Histidinol-phosphate aminotransferase family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidinol-phosphate aminotransferase 2
Similarity search - Component
Biological speciesRalstonia eutropha JMP134 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of histidinol-phosphate aminotransferase (YP_297314.1) from RALSTONIA EUTROPHA JMP134 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histidinol-phosphate aminotransferase 2
B: Histidinol-phosphate aminotransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,86823
Polymers80,9062
Non-polymers1,96221
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-43 kcal/mol
Surface area27530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.579, 93.433, 111.341
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA32 - 11832 - 118
21BB32 - 11832 - 118
12AA131 - 251131 - 251
22BB131 - 251131 - 251
13AA256 - 366256 - 366
23BB256 - 366256 - 366
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION

-
Components

#1: Protein Histidinol-phosphate aminotransferase 2 / Imidazole acetol-phosphate transaminase 2


Mass: 40453.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha JMP134 (bacteria) / Gene: YP_297314.1, hisC2, Reut_A3110 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100
References: UniProt: Q46WL3, histidinol-phosphate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979341
ReflectionResolution: 2.05→29.988 Å / Num. obs: 50845 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.759 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.13.60.7581.61349237080.758100
2.1-2.163.60.6591.81307836080.659100
2.16-2.223.60.5672.21278135230.567100
2.22-2.293.60.4652.61234234100.465100
2.29-2.373.60.3713.21218633480.371100
2.37-2.453.60.3053.91159532010.305100
2.45-2.543.60.2574.61126531000.257100
2.54-2.653.60.2175.51093730170.217100
2.65-2.763.60.196.21029828440.19100
2.76-2.93.60.167.7993327490.16100
2.9-3.063.60.1249.7954926510.124100
3.06-3.243.60.10112.2889924710.101100
3.24-3.473.60.08314.5850023660.083100
3.47-3.743.60.06617.1786221890.066100
3.74-4.13.60.05320724120220.053100
4.1-4.583.60.04722.2659118450.047100
4.58-5.293.50.05722.8577316480.057100
5.29-6.483.40.06223.4479613960.062100
6.48-9.173.40.04226.6377611210.04299.9
9.17-29.993.10.03627.419666280.03696.7

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.988 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 11.551 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.174
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. GOL AND SO4 MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. RESDIUES 22-23, 62-66, 118-123, 204 IN CHAIN A AND 41-42 IN CHAIN B ARE IN POOR ELECTRON DENSITY REGION.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2572 5.1 %RANDOM
Rwork0.194 ---
obs0.196 50789 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.3 Å2 / Biso mean: 51.396 Å2 / Biso min: 26.89 Å2
Baniso -1Baniso -2Baniso -3
1-4.16 Å20 Å20 Å2
2---1.81 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5358 0 119 378 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225669
X-RAY DIFFRACTIONr_bond_other_d0.0040.023790
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9937715
X-RAY DIFFRACTIONr_angle_other_deg1.38839257
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5945748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.01423.509228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95115896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711547
X-RAY DIFFRACTIONr_chiral_restr0.0920.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026315
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021100
X-RAY DIFFRACTIONr_nbd_refined0.1740.21099
X-RAY DIFFRACTIONr_nbd_other0.1420.23957
X-RAY DIFFRACTIONr_nbtor_refined0.1480.22725
X-RAY DIFFRACTIONr_nbtor_other0.0720.22905
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.10.2345
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.220
X-RAY DIFFRACTIONr_mcbond_it1.25724189
X-RAY DIFFRACTIONr_mcbond_other0.28421457
X-RAY DIFFRACTIONr_mcangle_it1.8845838
X-RAY DIFFRACTIONr_scbond_it3.73362150
X-RAY DIFFRACTIONr_scangle_it4.64381862
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1802MEDIUM POSITIONAL0.370.5
1853LOOSE POSITIONAL0.615
1802MEDIUM THERMAL1.092
1853LOOSE THERMAL2.1410
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 179 -
Rwork0.286 3523 -
all-3702 -
obs--100 %
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)
10.24120.11660.42260.63690.26980.7481-0.01820.0653-0.0112-0.10650.0007-0.085-0.01150.10370.0176-0.1558-0.01860.00340.00190.0087-0.007861.19650.578-0.427
20.1925-0.27470.22221.0073-0.19520.49690.03850.05560.0381-0.1114-0.0709-0.069-0.03430.0710.0324-0.18020.00150.0071-0.02930.009-0.014176.39133.9619.53
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 366
2X-RAY DIFFRACTION2B0 - 58
3X-RAY DIFFRACTION2B67 - 365

+
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