[English] 日本語
Yorodumi
- PDB-6an0: Crystal Structure of Histidinol Dehydrogenase from Elizabethkingi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6an0
TitleCrystal Structure of Histidinol Dehydrogenase from Elizabethkingia anophelis
ComponentsHistidinol dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Elizabethkingia anophelis NUHP1 / dehydrogenase / hisD / zinc binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


histidinol dehydrogenase / histidinol dehydrogenase activity / L-histidine biosynthetic process / NAD binding / zinc ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1300 / Histidinol dehydrogenase, conserved site / Histidinol dehydrogenase / Histidinol dehydrogenase, monofunctional / Histidinol dehydrogenase / Histidinol dehydrogenase signature. / Nitrogenase molybdenum iron protein domain / Aldehyde/histidinol dehydrogenase / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HISTIDINE / IODIDE ION / Histidinol dehydrogenase
Similarity search - Component
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of Histidinol Dehydrogenase from Elizabethkingia anophelis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09921
Polymers48,9171
Non-polymers2,18220
Water5,819323
1
A: Histidinol dehydrogenase
hetero molecules

A: Histidinol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,19842
Polymers97,8352
Non-polymers4,36340
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area16450 Å2
ΔGint-104 kcal/mol
Surface area31830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.520, 170.080, 65.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-861-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Histidinol dehydrogenase / / HDH


Mass: 48917.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Strain: NUHP1 / Gene: hisD, BD94_1332 / Plasmid: ElanA.18181.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077ECF2, histidinol dehydrogenase

-
Non-polymers , 5 types, 343 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1:1 21.3 mg/mL ElanA.18181.a.B1.PW3826 to MCSG1(e7) (20% w/v PEG3350, 0.2 M ammonium iodide, cryoprotection: 20% ethylene glycol, Tray 292598e7, puck ffs7-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 14, 2017 / Details: Beryllium Lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→31.449 Å / Num. obs: 39779 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.501 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.059 / Χ2: 1.029 / Net I/σ(I): 17.95 / Num. measured all: 218830 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.95.5750.5363.0729110.8810.589100
1.9-1.955.5850.3964.1728400.9270.436100
1.95-2.015.5980.3035.3827680.9530.33399.9
2.01-2.075.5780.2287.0927040.9730.2599.9
2.07-2.145.6140.1779.0826030.9850.19599.8
2.14-2.215.5840.1411.2825270.9890.15499.8
2.21-2.295.5470.11613.2924330.9930.12799.8
2.29-2.395.5760.09715.9623470.9940.10699.9
2.39-2.495.5590.08317.8422680.9960.09199.7
2.49-2.625.5280.0720.421660.9960.07799.9
2.62-2.765.4820.06123.2220530.9970.06899.8
2.76-2.935.4850.05425.9719510.9980.05999.6
2.93-3.135.4330.04928.3618420.9970.05599.6
3.13-3.385.4040.04132.7517160.9980.04599.1
3.38-3.75.3460.03835.1715670.9980.04298.8
3.7-4.145.3010.03536.7414350.9980.03998.9
4.14-4.785.3540.03238.4512640.9990.03598.5
4.78-5.855.2930.03137.6910720.9990.03597.6
5.85-8.275.1710.0337.428420.9990.03396.1
8.27-31.4494.8020.02737.464700.9990.0392

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K75

1k75


Resolution: 1.85→31.449 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1922 1970 4.95 %
Rwork0.1571 --
obs0.1588 39771 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.52 Å2 / Biso mean: 33.2508 Å2 / Biso min: 4.75 Å2
Refinement stepCycle: final / Resolution: 1.85→31.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 49 327 3629
Biso mean--54.78 41.44 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063377
X-RAY DIFFRACTIONf_angle_d0.7764592
X-RAY DIFFRACTIONf_chiral_restr0.055544
X-RAY DIFFRACTIONf_plane_restr0.005598
X-RAY DIFFRACTIONf_dihedral_angle_d13.7642063
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89630.27341440.213526562800100
1.8963-1.94760.25311440.199226812825100
1.9476-2.00490.25391260.188826972823100
2.0049-2.06960.2321430.173726792822100
2.0696-2.14350.21500.166426522802100
2.1435-2.22930.20741340.162126852819100
2.2293-2.33070.20781310.157626942825100
2.3307-2.45360.22371260.164927222848100
2.4536-2.60720.1991510.167426912842100
2.6072-2.80840.19061210.170927252846100
2.8084-3.09080.22751580.171526932851100
3.0908-3.53750.19681450.15822718286399
3.5375-4.45490.15081620.13052713287599
4.4549-31.45340.16091350.14132795293097
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)
11.1593-0.50861.02731.5338-1.54273.9652-0.1748-0.27970.45420.4076-0.02540.1914-0.4977-0.00870.20650.4812-0.0109-0.02840.399-0.26490.441818.494232.03074.1767
23.1947-0.9576-0.54542.05710.21291.26630.13210.45780.4723-0.3352-0.0304-0.1399-0.19770.0522-0.110.2639-0.05860.0570.24840.05850.228516.733737.2035-34.5677
35.60830.93020.61320.8111-0.03280.53610.18180.0689-0.44890.0142-0.0541-0.0880.190.1271-0.09380.26430.0289-0.01750.1771-0.050.19764.98956.8908-22.8526
41.3782-0.3038-0.53663.2439-0.63351.49570.00360.13590.1385-0.13210.0448-0.2377-0.03510.1802-0.04060.158-0.02360.02880.1984-0.00580.133214.927925.8868-29.9137
52.4648-1.93573.29392.596-3.34624.9205-0.0222-0.07640.10650.25340.0205-0.0801-0.19980.0512-0.02430.2204-0.00430.03060.1886-0.03570.174912.222727.3026-12.0625
62.68360.70760.70862.18270.05641.67830.0659-0.37340.06890.2429-0.0034-0.2573-0.05410.1425-0.06250.1997-0.0139-0.03850.2249-0.05190.184723.087820.29911.0463
72.8151-0.18320.96940.6570.01061.0350.0903-0.093-0.0890.02890.02050.09680.0637-0.1136-0.10840.2112-0.01020.01810.11390.02630.1444-8.108814.4296-16.7316
82.6572.72722.47544.0333.39053.85160.10520.2657-0.74262.77740.0096-0.33281.3708-0.1905-0.08210.95720.2103-0.11850.59750.07161.0227-3.17047.2963-23.8015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 26 )A-4 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 75 )A27 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 117 )A76 - 117
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 209 )A118 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 244 )A210 - 244
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 342 )A245 - 342
7X-RAY DIFFRACTION7chain 'A' and (resid 343 through 428 )A343 - 428
8X-RAY DIFFRACTION8chain 'E' and (resid 1 through 1 )E1

+
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