[English] 日本語
Yorodumi
- PDB-3nnk: Biochemical and Structural Characterization of a Ureidoglycine Am... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nnk
TitleBiochemical and Structural Characterization of a Ureidoglycine Aminotransferase in the Klebsiella pneumoniae Uric Acid Catabolic Pathway
ComponentsUreidoglycine-glyoxylate aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / PLP-DEPENDENT
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class V domain / Aminotransferase class-V / 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
Putative ureidoglycine-glyoxylate aminotransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsFrench, J.B. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: Biochemical and Structural Characterization of a Ureidoglycine Aminotransferase in the Klebsiella pneumoniae Uric Acid Catabolic Pathway.
Authors: French, J.B. / Ealick, S.E.
History
DepositionJun 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ureidoglycine-glyoxylate aminotransferase
B: Ureidoglycine-glyoxylate aminotransferase
C: Ureidoglycine-glyoxylate aminotransferase
D: Ureidoglycine-glyoxylate aminotransferase
E: Ureidoglycine-glyoxylate aminotransferase
F: Ureidoglycine-glyoxylate aminotransferase
G: Ureidoglycine-glyoxylate aminotransferase
H: Ureidoglycine-glyoxylate aminotransferase
J: Ureidoglycine-glyoxylate aminotransferase
K: Ureidoglycine-glyoxylate aminotransferase
L: Ureidoglycine-glyoxylate aminotransferase
M: Ureidoglycine-glyoxylate aminotransferase
O: Ureidoglycine-glyoxylate aminotransferase
P: Ureidoglycine-glyoxylate aminotransferase
R: Ureidoglycine-glyoxylate aminotransferase
S: Ureidoglycine-glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)735,33616
Polymers735,33616
Non-polymers00
Water17,150952
1
A: Ureidoglycine-glyoxylate aminotransferase
B: Ureidoglycine-glyoxylate aminotransferase
C: Ureidoglycine-glyoxylate aminotransferase
D: Ureidoglycine-glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)183,8344
Polymers183,8344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-90 kcal/mol
Surface area50420 Å2
MethodPISA
2
E: Ureidoglycine-glyoxylate aminotransferase
F: Ureidoglycine-glyoxylate aminotransferase
G: Ureidoglycine-glyoxylate aminotransferase
H: Ureidoglycine-glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)183,8344
Polymers183,8344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20480 Å2
ΔGint-86 kcal/mol
Surface area50420 Å2
MethodPISA
3
J: Ureidoglycine-glyoxylate aminotransferase
K: Ureidoglycine-glyoxylate aminotransferase
L: Ureidoglycine-glyoxylate aminotransferase
M: Ureidoglycine-glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)183,8344
Polymers183,8344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20560 Å2
ΔGint-85 kcal/mol
Surface area50300 Å2
MethodPISA
4
O: Ureidoglycine-glyoxylate aminotransferase
P: Ureidoglycine-glyoxylate aminotransferase
R: Ureidoglycine-glyoxylate aminotransferase
S: Ureidoglycine-glyoxylate aminotransferase


Theoretical massNumber of molelcules
Total (without water)183,8344
Polymers183,8344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20550 Å2
ΔGint-87 kcal/mol
Surface area50090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.150, 149.203, 197.996
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91J
101K
111L
121M
131O
141P
151R

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A-100 - 1000
2116B-100 - 1000
3116C-100 - 1000
4116D-100 - 1000
5116E-100 - 1000
6116F-100 - 1000
7116G-100 - 1000
8116H-100 - 1000
9116J-100 - 1000
10116K-100 - 1000
11116L-100 - 1000
12116M-100 - 1000
13116O-100 - 1000
14116P-100 - 1000
15116R-100 - 1000

-
Components

#1: Protein
Ureidoglycine-glyoxylate aminotransferase


Mass: 45958.480 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: MGH78578 / Gene: hpxJ / Production host: Escherichia coli (E. coli) / References: UniProt: B5B0L4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 34% MPD, 0.1 M NaCl, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.549
11h,-k,-l20.451
ReflectionResolution: 2.58→50 Å / Num. all: 575000 / Num. obs: 240000 / % possible obs: 96.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 2.4 % / Biso Wilson estimate: 33.6 Å2 / Rsym value: 0.131 / Net I/σ(I): 8.6
Reflection shellResolution: 2.58→2.65 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 12236 / Rsym value: 0.409 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJ0

1vj0


Resolution: 2.58→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 7.704 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24602 12213 5 %RANDOM
Rwork0.21738 ---
all0.21882 575000 --
obs0.21882 230218 93.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-1.82 Å2
2--21.79 Å20 Å2
3----21.37 Å2
Refinement stepCycle: LAST / Resolution: 2.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50682 0 0 952 51634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02151737
X-RAY DIFFRACTIONr_angle_refined_deg0.9921.96970131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.19356543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67122.9142258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.622158532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.24115472
X-RAY DIFFRACTIONr_chiral_restr0.0660.27739
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02139320
X-RAY DIFFRACTIONr_mcbond_it0.2071.532446
X-RAY DIFFRACTIONr_mcangle_it0.379251900
X-RAY DIFFRACTIONr_scbond_it0.319319291
X-RAY DIFFRACTIONr_scangle_it0.5654.518231
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3113 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.265
BLOOSE POSITIONAL0.235
CLOOSE POSITIONAL0.265
DLOOSE POSITIONAL0.255
ELOOSE POSITIONAL0.235
FLOOSE POSITIONAL0.225
GLOOSE POSITIONAL0.255
HLOOSE POSITIONAL0.235
JLOOSE POSITIONAL0.255
KLOOSE POSITIONAL0.225
LLOOSE POSITIONAL0.285
MLOOSE POSITIONAL0.275
OLOOSE POSITIONAL0.255
PLOOSE POSITIONAL0.245
RLOOSE POSITIONAL0.265
ALOOSE THERMAL3.5210
BLOOSE THERMAL1.7110
CLOOSE THERMAL2.3410
DLOOSE THERMAL1.2810
ELOOSE THERMAL3.1810
FLOOSE THERMAL1.5810
GLOOSE THERMAL1.9310
HLOOSE THERMAL1.610
JLOOSE THERMAL2.2510
KLOOSE THERMAL1.5610
LLOOSE THERMAL2.2310
MLOOSE THERMAL1.7810
OLOOSE THERMAL2.310
PLOOSE THERMAL1.3410
RLOOSE THERMAL2.310
LS refinement shellResolution: 2.583→2.65 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 653 -
Rwork0.406 12236 -
obs--67.84 %

+
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