[English] 日本語
Yorodumi
- PDB-3rp7: Crystal Structure of Klebsiella pneumoniae HpxO complexed with FA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rp7
TitleCrystal Structure of Klebsiella pneumoniae HpxO complexed with FAD and uric acid
Componentsflavoprotein monooxygenase
KeywordsOXIDOREDUCTASE / FAD-binding protein / monooxygenase
Function / homology
Function and homology information


FAD-dependent urate hydroxylase / FAD-dependent urate hydroxylase activity / urate oxidase activity / urate catabolic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / purine nucleobase metabolic process / FAD binding
Similarity search - Function
: / D-Amino Acid Oxidase; Chain A, domain 2 - #30 / : / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...: / D-Amino Acid Oxidase; Chain A, domain 2 - #30 / : / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / URIC ACID / FAD-dependent urate hydroxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.042 Å
AuthorsHicks, K.A. / O'Leary, S.E. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Mechanistic Studies of HpxO, a Novel Flavin Adenine Dinucleotide-Dependent Urate Oxidase from Klebsiella pneumoniae.
Authors: Hicks, K.A. / O'Leary, S.E. / Begley, T.P. / Ealick, S.E.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: flavoprotein monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3553
Polymers45,4021
Non-polymers9542
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.023, 67.840, 82.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein flavoprotein monooxygenase


Mass: 45401.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_16330, KPN_01663 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A6T923
#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 291 K / Method: hanging drop
Details: 0.05 M KH2PO4, 20% PEG 8000, hanging drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2009
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 24401 / Num. obs: 24401 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Χ2: 5.912 / Net I/σ(I): 22.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.115.60.31123831.335199.3
2.11-2.25.60.23823831.231100
2.2-2.35.70.19224141.5691100
2.3-2.425.60.1624281.9111100
2.42-2.575.60.12624192.2951100
2.57-2.775.60.10824043.3471100
2.77-3.055.60.0924544.7331100
3.05-3.495.60.07724418.092199.9
3.49-4.395.40.07248013.56199.5
4.39-5050.068259522.16198.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.042→33.92 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8481 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1229 5.05 %RANDOM
Rwork0.192 ---
obs0.194 24338 99.59 %-
all-24401 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.888 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 22.8971 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.518 Å20 Å20 Å2
2--1.7806 Å20 Å2
3---1.7374 Å2
Refinement stepCycle: LAST / Resolution: 2.042→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 65 194 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053027
X-RAY DIFFRACTIONf_angle_d1.0354123
X-RAY DIFFRACTIONf_chiral_restr0.068449
X-RAY DIFFRACTIONf_plane_restr0.004532
X-RAY DIFFRACTIONf_dihedral_angle_d12.8991061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.042-2.12380.24681270.19882492261998
2.1238-2.22040.30511260.191725462672100
2.2204-2.33750.22031530.188225162669100
2.3375-2.48390.26811250.193525522677100
2.4839-2.67560.23351350.19725542689100
2.6756-2.94470.25851390.198225712710100
2.9447-3.37050.22831420.191225652707100
3.3705-4.24510.2041330.181226122745100
4.2451-33.92470.2191490.19662701285099

+
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