[English] 日本語
Yorodumi
- PDB-2rdu: Crystal Structure of Human Glycolate Oxidase in Complex with Glyo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rdu
TitleCrystal Structure of Human Glycolate Oxidase in Complex with Glyoxylate
ComponentsHydroxyacid oxidase 1
KeywordsOXIDOREDUCTASE / GOX / HAOX1 / glycolate oxidase / hydroxy acid oxidase / glyoxylate / glyoxylic acid / Flavoprotein / FMN / Glycolate pathway / Peroxisome
Function / homology
Function and homology information


glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / peroxisomal matrix / glycine biosynthetic process / Peroxisomal protein import ...glyoxylate oxidase / glyoxylate oxidase activity / glycolate catabolic process / (S)-2-hydroxy-acid oxidase / fatty acid alpha-oxidation / (S)-2-hydroxy-acid oxidase activity / Glyoxylate metabolism and glycine degradation / peroxisomal matrix / glycine biosynthetic process / Peroxisomal protein import / peroxisome / FMN binding / response to oxidative stress / intracellular membrane-bounded organelle / cytosol
Similarity search - Function
Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Alpha-hydroxy acid dehydrogenase, FMN-dependent / FMN-dependent alpha-hydroxy acid dehydrogenase, active site / FMN hydroxy acid dehydrogenase domain / FMN-dependent alpha-hydroxy acid dehydrogenases active site. / FMN-dependent alpha-hydroxy acid dehydrogenase domain profile. / FMN-dependent dehydrogenase / FMN-dependent dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / GLYOXYLIC ACID / 2-Hydroxyacid oxidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsMurray, M.S. / Holmes, R.P. / Lowther, W.T.
CitationJournal: Biochemistry / Year: 2008
Title: Active Site and Loop 4 Movements within Human Glycolate Oxidase: Implications for Substrate Specificity and Drug Design.
Authors: Murray, M.S. / Holmes, R.P. / Lowther, W.T.
History
DepositionSep 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hydroxyacid oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1703
Polymers42,6401
Non-polymers5302
Water4,179232
1
A: Hydroxyacid oxidase 1
hetero molecules

A: Hydroxyacid oxidase 1
hetero molecules

A: Hydroxyacid oxidase 1
hetero molecules

A: Hydroxyacid oxidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,68212
Polymers170,5604
Non-polymers2,1228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.386, 97.386, 80.468
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Hydroxyacid oxidase 1 / HAOX1 / Glycolate oxidase / GOX


Mass: 42640.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HAO1, GOX1, HAOX1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: Q9UJM8, (S)-2-hydroxy-acid oxidase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE / Glyoxylic acid


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.24 Å3/Da / Density % sol: 45.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HEPES,PEG 600,glyoxylate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→30.8 Å / Num. obs: 44625 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 4.57 % / Rmerge(I) obs: 0.073 / Χ2: 0.98 / Net I/σ(I): 11.6 / Scaling rejects: 1541
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.65-1.713.080.4122.71228139900.8988.8
1.71-1.784.350.4063.41944244591.0199.2
1.78-1.864.60.3463.92093145261.1100
1.86-1.964.650.3134.32090444681.18100
1.96-2.084.690.2255.52129945081.08100
2.08-2.244.740.1676.92160945171.05100
2.24-2.464.790.1169.62175244980.99100
2.46-2.824.850.08614.42210345220.87100
2.82-3.554.880.04222.92226345350.78100
3.55-30.84.850.02935.52270746020.8199.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.8 Å
Translation2.5 Å30.8 Å

-
Processing

Software
NameVersionClassificationNB
d*TREK9.2Ldata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GOX
Resolution: 1.65→30.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 4.116 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2244 5 %RANDOM
Rwork0.181 ---
obs0.183 44620 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 36 232 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222897
X-RAY DIFFRACTIONr_angle_refined_deg1.351.9863926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83423.607122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42715514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8651524
X-RAY DIFFRACTIONr_chiral_restr0.110.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022155
X-RAY DIFFRACTIONr_nbd_refined0.2010.21523
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.214
X-RAY DIFFRACTIONr_mcbond_it0.8441.51851
X-RAY DIFFRACTIONr_mcangle_it1.20822886
X-RAY DIFFRACTIONr_scbond_it2.21931216
X-RAY DIFFRACTIONr_scangle_it3.4964.51038
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 152 -
Rwork0.322 2755 -
all-2907 -
obs--87.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.63950.54710.31831.01270.41610.45430.0435-0.0952-0.00620.1459-0.0670.01540.051-0.03940.02350.08830.00770.02440.08480.00650.013514.771-11.793-11.635
20.83260.1332-0.16250.8196-0.11580.27570.00960.0142-0.17730.08420.0199-0.25470.04710.0666-0.02950.06130.0132-0.01890.04560.00340.061131.996-20.681-16.85
31.0182-0.5599-0.56731.77240.42991.1496-0.0189-0.25280.09680.27250.136-0.4649-0.0140.2389-0.11710.0455-0.0106-0.0570.0868-0.0180.104138.069-6.061-11.347
40.51940.26230.08741.59470.21580.2665-0.01580.07850.0083-0.18620.0543-0.1977-0.02590.0664-0.03850.0569-0.00090.02410.0658-0.00130.018127.511-8.946-27.012
51.87820.52161.18371.15960.41942.24830.02930.0543-0.13640.0382-0.0039-0.02590.0804-0.0246-0.02540.06060.00340.02620.0430.00710.036415.699-23.965-18.069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 5420 - 71
2X-RAY DIFFRACTION2AA55 - 14072 - 157
3X-RAY DIFFRACTION3AA141 - 202158 - 219
4X-RAY DIFFRACTION4AA203 - 315220 - 332
5X-RAY DIFFRACTION5AA316 - 362333 - 379

+
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