[English] 日本語
Yorodumi
- PDB-1jro: Crystal Structure of Xanthine Dehydrogenase from Rhodobacter caps... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jro
TitleCrystal Structure of Xanthine Dehydrogenase from Rhodobacter capsulatus
Components(xanthine dehydrogenase, chain ...) x 2
KeywordsOXIDOREDUCTASE / Partial Beta-Barrel / xdh / xo
Function / homology
Function and homology information


1.1.1.204 / xanthine dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding
Similarity search - Function
Xanthine dehydrogenase, small subunit, bacteria / Xanthine dehydrogenase, molybdopterin binding subunit / Xanthine dehydrogenase, small subunit / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal ...Xanthine dehydrogenase, small subunit, bacteria / Xanthine dehydrogenase, molybdopterin binding subunit / Xanthine dehydrogenase, small subunit / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding domain / CO dehydrogenase flavoprotein C-terminal domain / Aldehyde Oxidoreductase; domain 4 / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain / Molybdopterin dehydrogenase, FAD-binding / CO dehydrogenase flavoprotein, C-terminal / CO dehydrogenase flavoprotein, C-terminal domain superfamily / FAD binding domain in molybdopterin dehydrogenase / CO dehydrogenase flavoprotein C-terminal domain / CO dehydrogenase flavoprotein, C-terminal domain / Aldehyde oxidase/xanthine dehydrogenase / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead / [2Fe-2S]-binding / Aldehyde oxidase/xanthine dehydrogenase, first molybdopterin binding domain / Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead superfamily / [2Fe-2S]-binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain superfamily / Aldehyde oxidase/xanthine dehydrogenase, second molybdopterin binding domain / [2Fe-2S] binding domain / Molybdopterin cofactor-binding domain / Molybdopterin cofactor-binding domain / Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / Aldehyde Oxidoreductase; domain 3 / FAD-binding, type PCMH, subdomain 1 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / Beta-grasp domain / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2Fe-2S iron-sulfur cluster binding domain / Enolase-like; domain 1 / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / DNA polymerase; domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / DIOXOTHIOMOLYBDENUM(VI) ION / Chem-MTE / : / : / Xanthine dehydrogenase / Xanthine dehydrogenase
Similarity search - Component
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTruglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C.
CitationJournal: Structure / Year: 2002
Title: Crystal structures of the active and alloxanthine-inhibited forms of xanthine dehydrogenase from Rhodobacter capsulatus
Authors: Truglio, J.J. / Theis, K. / Leimkuhler, S. / Rappa, R. / Rajagopalan, K.V. / Kisker, C.
History
DepositionAug 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 22, 2015Group: Non-polymer description
Revision 1.4Aug 16, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_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: xanthine dehydrogenase, chain A
B: xanthine dehydrogenase, chain B
C: xanthine dehydrogenase, chain A
D: xanthine dehydrogenase, chain B
E: xanthine dehydrogenase, chain A
F: xanthine dehydrogenase, chain B
G: xanthine dehydrogenase, chain A
H: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)536,23632
Polymers529,3028
Non-polymers6,93524
Water2,216123
1
A: xanthine dehydrogenase, chain A
B: xanthine dehydrogenase, chain B
C: xanthine dehydrogenase, chain A
D: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,11816
Polymers264,6514
Non-polymers3,46712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24380 Å2
ΔGint-197 kcal/mol
Surface area76990 Å2
MethodPISA
2
E: xanthine dehydrogenase, chain A
F: xanthine dehydrogenase, chain B
G: xanthine dehydrogenase, chain A
H: xanthine dehydrogenase, chain B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,11816
Polymers264,6514
Non-polymers3,46712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24420 Å2
ΔGint-201 kcal/mol
Surface area76840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.875, 141.053, 158.113
Angle α, β, γ (deg.)109.53, 105.83, 101.33
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

-
Components

-
Xanthine dehydrogenase, chain ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
xanthine dehydrogenase, chain A / E.C.1.1.1.204 / XD


Mass: 49347.453 Da / Num. of mol.: 4 / Fragment: chain A, residues 1-462
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 2956674, UniProt: O54050*PLUS, 1.1.1.204
#2: Protein
xanthine dehydrogenase, chain B / E.C.1.1.1.204 / XD


Mass: 82978.031 Da / Num. of mol.: 4 / Fragment: chain B, residues 1-777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Production host: Escherichia coli (E. coli) / References: EMBL: 13397863, UniProt: O54051*PLUS, 1.1.1.204

-
Non-polymers , 6 types, 147 molecules

#3: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2S2
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MTE / PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER


Mass: 395.352 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O6PS2
#7: Chemical
ChemComp-MOS / DIOXOTHIOMOLYBDENUM(VI) ION


Mass: 161.012 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: HMoO2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG, Tris, DTT, isopropanol at pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
28 %PEG80001reservoir
37.5 mM1reservoirBaCl2
425 mMdithiothreitol1reservoir
53 %isopropanol1reservoir
60.1 MTris1reservoirpH8.0

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 14, 2001
CUSTOM-MADE2CCDMar 12, 2001
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 187987 / Num. obs: 187987 / % possible obs: 99.2 % / Observed criterion σ(I): -1000 / Redundancy: 3.8 % / Rsym value: 0.17 / Net I/σ(I): 11.2
Reflection shellResolution: 2.7→2.8 Å / % possible obs: 98 % / Mean I/σ(I) obs: 2.7 / Rsym value: 0.73
Reflection
*PLUS
Num. measured all: 722868 / Rmerge(I) obs: 0.161
Reflection shell
*PLUS
Rmerge(I) obs: 0.73

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO4

1fo4


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.3 / SU ML: 0.2 / SU Rfree: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.6
Details: FOUR-FOLD NCS RESTRAINTS WERE IMPOSED ON CHAINS A, B, C, D AND E, F, G, H
RfactorNum. reflection% reflectionSelection details
Rfree0.25154 9424 5 %RANDOM
Rwork0.21311 ---
all0.215 178563 --
obs0.21505 178563 99.18 %-
Solvent computationSolvent model: BABINET MODEL WITH MAS
Displacement parametersBiso mean: 39.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20.3 Å20.37 Å2
2---1.57 Å2-0.91 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36348 0 360 123 36831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02137259
X-RAY DIFFRACTIONr_angle_refined_deg2.3461.950687
X-RAY DIFFRACTIONr_chiral_restr0.1420.25652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0228808
X-RAY DIFFRACTIONr_nbd_refined0.1770.53190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.53190
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.317820
X-RAY DIFFRACTIONr_mcbond_it1.0681.523984
X-RAY DIFFRACTIONr_mcangle_it2.03238100
X-RAY DIFFRACTIONr_scbond_it3.409313275
X-RAY DIFFRACTIONr_scangle_it5.5764.512571
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 688
Rwork0.286 13129
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.67 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.025
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.365
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.286

+
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