[English] 日本語
Yorodumi
- PDB-4grx: Structure of an omega-aminotransferase from Paracoccus denitrificans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4grx
TitleStructure of an omega-aminotransferase from Paracoccus denitrificans
ComponentsAminotransferase
KeywordsTRANSFERASE / class III transaminase
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
DELTA-AMINO VALERIC ACID / Aminotransferase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsRausch, C. / Lerchner, A. / Schiefner, A. / Skerra, A.
CitationJournal: Proteins / Year: 2013
Title: Crystal structure of the omega-aminotransferase from Paracoccus denitrificans and its phylogenetic relationship with other class III aminotransferases that have biotechnological potential.
Authors: Rausch, C. / Lerchner, A. / Schiefner, A. / Skerra, A.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,77510
Polymers206,4464
Non-polymers3286
Water4,414245
1
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3875
Polymers103,2232
Non-polymers1643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-98 kcal/mol
Surface area28700 Å2
MethodPISA
2
C: Aminotransferase
D: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3875
Polymers103,2232
Non-polymers1643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10730 Å2
ΔGint-97 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 103.630, 145.430
Angle α, β, γ (deg.)90.000, 98.880, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two dimer A/B and C/D.

-
Components

#1: Protein
Aminotransferase


Mass: 51611.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: Pd1222 / Gene: Pden_3984 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21
References: UniProt: A1B956, Transferases; Transferring nitrogenous groups; Transaminases
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-DAV / DELTA-AMINO VALERIC ACID


Mass: 118.154 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25 %(w/v) PEG3350, 0.4 M NaCl, 10 mM urea, 0.1 M Tris/HCl, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2009 / Details: Double Crystal
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 60091 / Num. obs: 60091 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.039 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.31
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.6-2.70.5582.76241596386199.6
2.7-2.80.4453.392133455711100
2.8-30.3164.743438189671100
3-3.50.1598.915536414496199.8
3.5-40.07318.09306408106199.6
4-60.04227.994443111693199.8
6-80.03531.17108232873199.7
8-100.02242.4838241030199.6
10-200.01946.093470969186.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model was build with MODELLER using PDB entries 3GJU, 3I5T, and 3HMU.

3gju

3i5t

3hmu


Resolution: 2.6→19.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.1952 / WRfactor Rwork: 0.1511 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8445 / SU B: 22.88 / SU ML: 0.231 / SU R Cruickshank DPI: 0.2489 / SU Rfree: 0.3015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 3063 5.1 %RANDOM
Rwork0.1784 ---
all0.1809 60090 --
obs0.1809 60090 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.11 Å2 / Biso mean: 38.2066 Å2 / Biso min: 12.86 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å2-0 Å2-0.03 Å2
2---2.41 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14012 0 20 245 14277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914394
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9619530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80451792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64823.313640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.208152272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1741596
X-RAY DIFFRACTIONr_chiral_restr0.090.22084
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111112
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 231 -
Rwork0.254 4014 -
all-4245 -
obs--99.81 %
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)
11.92870.48570.01432.4544-0.25731.46360.0094-0.06020.0040.11240.0950.3472-0.2796-0.2256-0.10450.08960.0831-0.02660.17540.05610.2323-2.391435.263764.6429
21.28980.11580.7251.48610.25711.53660.00030.0587-0.0644-0.12630.10820.20520.1648-0.0662-0.10850.1001-0.0034-0.04770.0810.04190.11269.7299.994864.4594
31.7985-1.41580.80951.5434-0.75151.40770.1214-0.0193-0.1136-0.07320.11760.35340.2245-0.2074-0.2390.0536-0.0416-0.03040.20740.0750.2915-2.393912.523665.5347
42.022-0.7707-0.10793.5254-0.75931.6646-0.0538-0.2307-0.10450.31740.14950.5281-0.1376-0.5443-0.09570.04480.019-0.01070.25160.0910.3323-6.504219.890665.6329
50.56120.8496-0.31351.91320.21761.3198-0.14570.139-0.0421-0.43240.1378-0.00120.08330.03780.00790.25960.0558-0.11820.26430.05950.17476.386624.572244.4076
630.4162-2.3577-10.65342.0035-0.24214.8548-0.11241.2537-0.0346-0.60710.28150.25820.0377-0.5144-0.1690.5584-0.1514-0.14420.33140.0180.1440.190930.708938.8075
70.961.26440.18192.16220.65080.38070.03450.0513-0.12310.4882-0.08970.00890.3609-0.15420.05530.580.08140.12620.68510.1640.6649-10.246423.013390.0643
81.82170.0014-0.06970.64720.82742.12410.0076-0.05870.05220.1816-0.00050.3055-0.0011-0.3257-0.00710.19620.11750.09160.12580.08240.3604-0.719441.280176.2684
90.70360.3124-0.01841.80890.46072.1939-0.0317-0.1108-0.03110.3970.0156-0.05-0.11240.20860.01610.15250.0267-0.04120.11570.01770.082122.341531.822785.3046
102.9688-1.26610.26863.34260.94680.4274-0.01290.0561-0.05460.125-0.03090.15990.0335-0.00830.04380.21470.037-0.05820.13820.06640.075514.232538.077572.0596
111.456-0.1788-0.03071.9446-0.61340.31680.0248-0.19540.13670.61930.11840.2578-0.3709-0.1178-0.14320.46070.15570.11910.09920.03460.17887.130140.81991.7314
121.0713-0.19711.18872.8894-2.59453.31690.1651-0.2487-0.24450.47120.25360.325-0.2228-0.4182-0.41880.49610.08730.17940.32560.10620.39960.574431.9918104.4975
131.916-0.58390.48022.8619-0.80943.4913-0.032-0.24170.13210.09350.11210.1788-0.2946-0.2525-0.080.219-0.0019-0.00810.1211-0.05090.1342-25.760461.014122.5101
142.23910.0187-1.18814.29750.58651.90120.04740.2358-0.0828-0.23770.0369-0.6588-0.05380.4632-0.08420.05550.0074-0.05240.4301-0.01190.3779-2.272147.400413.1139
150.89820.30760.13161.4508-0.14932.1223-0.0639-0.0068-0.16670.0290.0012-0.17330.28060.06580.06270.17210.05680.01170.1006-0.01560.1837-25.179229.265413.2472
161.37351.2534-0.55832.13390.37751.2144-0.0642-0.0543-0.1108-0.10090.0464-0.32140.09840.22680.01780.16190.08660.01220.26530.02470.294-12.626636.262517.6866
171.38170.37050.00281.83770.26530.0587-0.07540.1819-0.303-0.48730.1415-0.4377-0.04570.1078-0.06610.23650.07670.01180.494-0.01780.4086-6.667938.724811.2381
181.62171.2759-0.66331.9104-0.25580.66990.0855-0.22850.08650.2367-0.11030.1883-0.0366-0.06360.02480.25190.0366-0.05240.266-0.00510.1419-30.388845.420635.3713
190.9428-0.6214-0.40381.6505-0.63991.3250.0057-0.0094-0.2209-0.5479-0.0391-0.35210.50030.36650.03340.3796-0.00210.10220.6624-0.10090.67823.530345.3241-1.4147
200.7245-0.07560.18380.8970.06751.4473-0.0227-0.03260.11-0.07820.0209-0.1257-0.14630.09420.00190.165-0.03720.03150.1262-0.02550.1497-22.487755.94924.4561
210.85370.1064-0.13071.3487-0.34351.68490.00860.40680.0044-0.32620.0104-0.1108-0.08560.0422-0.0190.3504-0.0030.04120.2478-0.03030.1291-25.508553.0023-15.796
221.0644-0.40730.61031.18180.46810.9802-0.0205-0.01820.0766-0.22730.0656-0.1991-0.27340.1842-0.04510.3166-0.06260.05630.17930.01130.1918-18.770660.99272.1657
230.78130.5291.09341.44151.88822.7840.22250.3558-0.34470.03730.115-0.11140.16090.5122-0.33740.4508-0.00620.13950.6366-0.04760.4559-2.706950.0578-21.3867
240.70290.8508-1.6481.2167-2.37664.72790.19960.1676-0.01910.0433-0.0928-0.0485-0.18580.3852-0.10680.5042-0.00020.22680.9384-0.15890.73095.400555.496-17.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 106
2X-RAY DIFFRACTION2A107 - 238
3X-RAY DIFFRACTION3A239 - 301
4X-RAY DIFFRACTION4A302 - 366
5X-RAY DIFFRACTION5A367 - 429
6X-RAY DIFFRACTION6A430 - 453
7X-RAY DIFFRACTION7B5 - 41
8X-RAY DIFFRACTION8B42 - 109
9X-RAY DIFFRACTION9B110 - 282
10X-RAY DIFFRACTION10B283 - 314
11X-RAY DIFFRACTION11B315 - 388
12X-RAY DIFFRACTION12B389 - 453
13X-RAY DIFFRACTION13C5 - 58
14X-RAY DIFFRACTION14C59 - 106
15X-RAY DIFFRACTION15C107 - 265
16X-RAY DIFFRACTION16C266 - 301
17X-RAY DIFFRACTION17C302 - 350
18X-RAY DIFFRACTION18C351 - 453
19X-RAY DIFFRACTION19D5 - 60
20X-RAY DIFFRACTION20D61 - 159
21X-RAY DIFFRACTION21D160 - 283
22X-RAY DIFFRACTION22D284 - 357
23X-RAY DIFFRACTION23D358 - 426
24X-RAY DIFFRACTION24D427 - 453

+
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://pdbjlvh1.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