[English] 日本語
Yorodumi
- PDB-6vtv: Crystal structure of PuuD gamma-glutamyl-gamma-aminobutyrate hydr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vtv
TitleCrystal structure of PuuD gamma-glutamyl-gamma-aminobutyrate hydrolase from E. coli
ComponentsGamma-glutamyl-gamma-aminobutyrate hydrolase PuuD
KeywordsHYDROLASE / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / PUTRESCINE / PUTRESCINE UTILIZATION PATHWAY / GAMMA-GLUTAMYL-GAMMA-AMINOBUTYRATE / PEPTIDASE C26 FAMILY / ALPHA/BETA PROTEIN
Function / homology
Function and homology information


gamma-glutamyl-gamma-aminobutyrate hydrolase / gamma-glutamyl-gamma-aminobutyrate hydrolase activity / putrescine catabolic process / polyamine catabolic process
Similarity search - Function
Peptidase C26 / Peptidase C26 / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
: / Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsStogios, P.J. / EVDOKIMOVA, E. / DI LEO, R. / SAVCHENKO, A. / JOACHIMIAK, A. / SATCHELL, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: PuuD gamma-glutamyl-gamma-aminobutyrate hydrolase
Authors: Stogios, P.J.
History
DepositionFeb 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD
B: Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1754
Polymers57,0652
Non-polymers1102
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-34 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.161, 72.177, 98.631
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD / Gamma-Glu-GABA hydrolase


Mass: 28532.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: puuD, ycjL, b1298, JW1291 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold
References: UniProt: P76038, gamma-glutamyl-gamma-aminobutyrate hydrolase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M calcium chloride, 0.1 M Tris pH 8.5, 25% (w/v) PEG3350, 1 mM manganese chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→23 Å / Num. obs: 30884 / % possible obs: 98.6 % / Redundancy: 6.3 % / Biso Wilson estimate: 28.26 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.037 / Net I/σ(I): 21.3
Reflection shellResolution: 2.06→2.1 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1474 / CC1/2: 0.832 / Rpim(I) all: 0.261 / % possible all: 95.5

-
Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FIJ

3fij


Resolution: 2.06→22.93 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.151
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1913 6.5 %RANDOM
Rwork0.1732 ---
obs0.1761 29431 94.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.35 Å2
Refinement stepCycle: LAST / Resolution: 2.06→22.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3886 0 2 525 4413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263989
X-RAY DIFFRACTIONf_angle_d0.53765437
X-RAY DIFFRACTIONf_chiral_restr0.0443603
X-RAY DIFFRACTIONf_plane_restr0.0042728
X-RAY DIFFRACTIONf_dihedral_angle_d19.65291497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.110.31821210.23331741X-RAY DIFFRACTION84.22
2.11-2.170.30911270.22441822X-RAY DIFFRACTION88.59
2.17-2.230.26211320.20951883X-RAY DIFFRACTION91.42
2.23-2.30.23981310.20441887X-RAY DIFFRACTION92.19
2.3-2.380.25211420.20151891X-RAY DIFFRACTION92.07
2.38-2.480.25371260.20391912X-RAY DIFFRACTION92.59
2.48-2.590.24171350.1911938X-RAY DIFFRACTION93.46
2.59-2.730.2581330.19041961X-RAY DIFFRACTION95.23
2.73-2.90.2081390.18872002X-RAY DIFFRACTION95.58
2.9-3.120.23541490.18422048X-RAY DIFFRACTION97.82
3.12-3.440.19951400.17272052X-RAY DIFFRACTION97.81
3.44-3.930.19791380.14372058X-RAY DIFFRACTION97.95
3.93-4.940.17081480.12922115X-RAY DIFFRACTION98.73
4.94-22.930.20481520.1742208X-RAY DIFFRACTION98.7
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)
16.375771862292.004642771352.580785748147.15650534652.182828548664.31248587147-0.00454112329255-0.0618116004058-0.00264871105870.2180968174680.180270416704-0.258946477545-0.09708191313690.201194199578-0.2252542007210.152652021189-0.01817548934770.0377556191970.251061801861-6.53570435039E-50.29333999594442.476635818534.949744015240.2478497872
23.616966532990.101748531713-0.9619236752261.926804381360.1355522413381.5703007756-0.06678050130440.0449181292010.0261839716766-0.05222807334480.07161689295410.06789583609720.04173788299960.0385131699539-0.01423058391510.172690776291-0.00414038906411-0.01707943038170.1590401798890.004217755512930.18685647004736.807129460836.644792985138.9397153172
33.16155707985-0.0806567744125-0.7958937306254.499707824454.200474773546.22767260449-0.04537607877230.1134666807980.3144690148670.081856580025-0.07359724921380.1623205882090.166315139861-0.6935685334550.1272346231970.198185879921-0.03263129354760.019636833440.2322331851460.03766347092650.36270915820430.735859970940.759061138838.6977225605
43.447042249110.745520101487-1.158024550463.05656478155-0.9618157171153.60498743749-0.0178403842126-0.1845589998880.1035277583750.390146537414-0.06733873195020.339010131606-0.0467987303772-0.2482079276680.06986043394250.22320409469-0.03125615799520.03029991113930.221447071946-0.06126197572710.27216032883723.149468872732.318482646946.5286055708
53.365599124-0.380207175716-1.386085734231.85770097085-0.1051356504812.12223824435-0.2241639288580.193908147151-0.4179415706380.0002361473156810.01719142139270.0636984576680.456752185722-0.1341219198650.1647812772550.306816077109-0.05040788163820.02983814254890.196358158341-0.05859080275370.28105309334326.244156174122.25707908841.796099788
68.48762598363-2.060618406612.265147430514.80786491424-4.604872812084.581807285150.2871678254961.0940022294-0.908810000174-3.062161147050.4821620744460.684665339660.2349719538840.0816359556629-0.7788431745770.943503475327-0.0165124582172-0.04660136338430.644540622142-0.0985750597490.50057291050133.592977643129.1925234315.2515984414
73.73804909949-0.2711161774210.356280599944.17712746137-0.1365847743783.969893331640.02989192248720.187163540324-0.0438304874215-0.1694130743070.0764579517928-0.120801436118-0.0601796441828-0.0405773439782-0.102614810540.1269909409560.02086992201340.004636040868670.1998621360340.01034993148590.19779506592750.141958463237.66186995936.004304648
84.16417175849-0.1789120206791.5701618213.95932927266-2.219376622045.185137581010.125256380160.0174461172797-0.354984306533-0.0765729121158-0.0734676906637-0.03978623959470.324982062890.0518864908664-0.07592135100620.207347775780.05049333175890.02260960786790.206533315987-0.03175482060030.32290807198263.632064408830.944242392538.4714788189
93.13481031965-1.041084769140.4411984909024.000736017780.1958035813753.43848923151-0.0277825477765-0.2211891166370.3076857606120.2374267756070.0756705186045-0.224689758356-0.1231581588810.126300887018-0.04415767906810.1697076548190.002074440527190.01100100798290.248360975721-0.00935269912310.2753217699867.670947289646.224436722144.435730504
102.72586061143-0.862977775716-0.6415559900541.413206317511.542893764133.123796029840.07823362291810.2248737814020.573142858532-0.182473437636-0.00535003709284-0.167877564044-0.2208102305690.121411176269-0.05113836207730.2480821130490.00699217755460.05097857056980.2274197383760.04364593666140.33642763019670.592738514547.490528193538.9900975999
113.76071560334-0.3484157773491.398808169122.605641159651.510452034383.902109863990.04306346844710.4434996680830.487484748962-0.256330945389-0.0999944559003-0.063876169739-0.3036171523070.01923217080950.04851047574140.218169961463-0.006864036834740.0518162506120.2167657625260.08230214352240.28843934445762.706155654849.366834930234.4626873886
126.593333672747.587203027613.808048079172.00004435986.111149311872.69308300440.5939272097073.02107022313-0.70939811937-2.619591760150.521938626428-0.7431627635560.4254919693930.936491571131-0.7963978781210.6583082453430.230567294985-0.05017203594671.02171694124-0.01319801615660.47367982692755.025462543942.568205016714.12826286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:24)
2X-RAY DIFFRACTION2(chain A and resid 25:88)
3X-RAY DIFFRACTION3(chain A and resid 89:110)
4X-RAY DIFFRACTION4(chain A and resid 111:146)
5X-RAY DIFFRACTION5(chain A and resid 147:252)
6X-RAY DIFFRACTION6(chain A and resid 253:258)
7X-RAY DIFFRACTION7(chain B and resid 7:76)
8X-RAY DIFFRACTION8(chain B and resid 77:113)
9X-RAY DIFFRACTION9(chain B and resid 114:176)
10X-RAY DIFFRACTION10(chain B and resid 177:199)
11X-RAY DIFFRACTION11(chain B and resid 200:251)
12X-RAY DIFFRACTION12(chain B and resid 252:257)

+
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