[English] 日本語
Yorodumi
- PDB-4gxw: Crystal structure of a cog1816 amidohydrolase (target EFI-505188)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gxw
TitleCrystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn
ComponentsAdenosine deaminase
KeywordsHYDROLASE / amidohydrolase / cog1816 / adenosine deaminase related protein / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


adenine deaminase activity / adenine catabolic process / adenosine deaminase / hypoxanthine salvage / metal ion binding / cytosol
Similarity search - Function
Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsVetting, M.W. / Goble, A.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal structure of a cog1816 amidohydrolase (target EFI-505188) from Burkhoderia ambifaria, with bound Zn
Authors: Vetting, M.W. / Goble, A.M. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Imker, H.J. / Raushel, F.M. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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_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: Adenosine deaminase
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5986
Polymers85,3962
Non-polymers2024
Water23,5821309
1
A: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7642
Polymers42,6981
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8344
Polymers42,6981
Non-polymers1363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.058, 66.223, 75.432
Angle α, β, γ (deg.)90.000, 93.640, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Adenosine deaminase


Mass: 42698.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (bacteria) / Strain: AMMD / Gene: Bamb_4621 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B6Q2, adenosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1309 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.5
Details: Protein (20 mM Hepes pH 7.5; Reservoir (0.2 M magnesium chloride, 0.1 M MES pH 6.5, 10% Peg4000); Cryoprotection (Reservoir, + 20% Diethylene glycol), sitting drop vapor diffusion, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Aug 13, 2012 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.3→75.28 Å / Num. all: 175186 / Num. obs: 175186 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.372.90.5671.372987251880.56798.3
1.37-1.453.50.4261.883478241790.42699.7
1.45-1.553.50.2722.780242227170.27299.8
1.55-1.683.60.1784.276502212410.17899.9
1.68-1.843.70.1196.371758195940.11999.9
1.84-2.063.70.089.365330176820.0899.9
2.06-2.373.70.05812.357934155900.05899.8
2.37-2.913.70.04315.348712132120.04399.6
2.91-4.113.60.03417.537009101840.03499
4.11-75.283.60.02918.32008255990.02997.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PAO

3pao


Resolution: 1.3→29.257 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.8988 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1814 8755 5 %RANDOM
Rwork0.1601 ---
all0.1612 175099 --
obs0.1612 175099 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.17 Å2 / Biso mean: 16.8155 Å2 / Biso min: 6.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→29.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5794 0 4 1309 7107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086106
X-RAY DIFFRACTIONf_angle_d1.0818354
X-RAY DIFFRACTIONf_chiral_restr0.075885
X-RAY DIFFRACTIONf_plane_restr0.0061116
X-RAY DIFFRACTIONf_dihedral_angle_d12.092209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.31480.29342580.26375327558595
1.3148-1.33020.26132860.25155411569798
1.3302-1.34650.25543110.23745543585499
1.3465-1.36350.23173060.222254875793100
1.3635-1.38140.23263010.210855245825100
1.3814-1.40040.22322760.205155275803100
1.4004-1.42040.23292520.200155685820100
1.4204-1.44160.20262970.190555975894100
1.4416-1.46410.21382700.182955225792100
1.4641-1.48810.1922950.17555345829100
1.4881-1.51380.19293410.169855405881100
1.5138-1.54130.17852950.163155805875100
1.5413-1.57090.19932990.156255045803100
1.5709-1.6030.16412810.149455445825100
1.603-1.63780.19023050.149755325837100
1.6378-1.67590.17912810.146655905871100
1.6759-1.71790.16872800.147455735853100
1.7179-1.76430.16323130.147155305843100
1.7643-1.81620.18012790.149155885867100
1.8162-1.87480.16173020.152655595861100
1.8748-1.94180.20962980.165655675865100
1.9418-2.01950.18243020.146755775879100
2.0195-2.11140.16212910.143655455836100
2.1114-2.22270.16762780.145356185896100
2.2227-2.36190.17932910.157455815872100
2.3619-2.54420.17272870.148655755862100
2.5442-2.80.17552860.148855925878100
2.8-3.20480.1652800.15475566584699
3.2048-4.0360.1563240.14395546587099
4.036-29.26490.1712900.15295597588797
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)
10.75420.4457-0.30120.864-0.00120.2606-0.01110.01280.186-0.00470.0290.2527-0.0425-0.0889-0.01230.1090.0036-0.00480.1190.00060.1764-50.1011-26.150417.9899
20.84020.3340.06810.75270.3641.55940.0466-0.05680.6487-0.3019-0.28830.3312-0.5107-0.02740.1420.27710.0456-0.01090.2171-0.14350.4488-35.7999-11.030327.6873
30.79460.35360.21020.46890.15150.33650.0139-0.09580.02570.0461-0.02670.0269-0.0225-0.02620.01090.1037-0.01110.00230.1204-0.00630.0817-29.7828-27.052728.1531
40.7261-0.2047-0.13640.29270.22810.90180.0053-0.03280.00750.00780.0036-0.03740.02190.1069-0.00570.084-0.0032-0.00410.0929-0.00060.0888-22.4015-30.836114.0631
50.9205-0.0097-0.17230.9113-0.11280.5753-0.01790.11860.0139-0.08890.01110.06970.0145-0.02270.00710.0971-0.0082-0.00540.09880.00130.0899-34.7791-28.83251.884
61.02650.2935-0.26410.9316-0.14880.4443-0.01940.02740.0457-0.02320.01410.09840.0129-0.07230.00440.0879-0.0062-0.01510.0933-0.00230.1128-48.7817-32.618312.6582
70.24720.2539-0.08520.5301-0.150.4098-0.0004-0.03050.03890.00580.04830.1434-0.0305-0.1725-0.04660.09710.00760.0050.13820.00960.1183-13.2258.178218.0184
80.8801-0.41930.62790.7851-0.56720.935-0.0375-0.10660.26310.07-0.0308-0.1553-0.2127-0.01210.04810.16490.01170.00410.1469-0.03620.15843.772821.686633.0425
90.66940.0165-0.04170.37610.09580.61240.007-0.0873-0.01680.0272-0.0086-0.00850.0040.00220.00490.0818-0.0029-0.0050.08430.00420.06857.80825.887924.7637
100.8772-0.047-0.23730.31580.03430.9692-0.0052-0.0297-0.06550.00350.0002-0.00340.020.08330.00060.08310.0030.0060.07610.00090.080813.52551.446111.2141
110.7793-0.2251-0.24950.76210.2150.46010.00860.1208-0.0193-0.1065-0.03640.0228-0.0144-0.04330.02520.11350.0033-0.00350.0989-0.00060.0851.82625.02242.1571
120.3245-0.5898-0.31992.60111.11250.4970.10240.16590.0495-0.2639-0.06890.1541-0.1384-0.1268-0.02840.14360.0263-0.00860.13230.01530.1196-10.596313.62812.5384
130.64280.12770.05980.3304-0.1760.61990.0095-0.0082-0.0063-0.02620.00620.03110.0553-0.0996-0.01630.0929-0.0049-0.00630.09490.00780.0925-9.84322.692313.1162
141.6064-0.3376-0.04861.3911-0.0951.0988-0.02030.0267-0.0527-0.08560.02650.10740.2102-0.24110.00950.1675-0.0655-0.00670.16050.01980.1729-15.3423-10.255417.0909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 42 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 75 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 147 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 148 through 216 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 273 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 274 through 371 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 42 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 65 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 176 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 216 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 217 through 273 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 274 through 291 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 292 through 341 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 342 through 366 )B0

+
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