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- PDB-6vtv: Crystal structure of PuuD gamma-glutamyl-gamma-aminobutyrate hydr... -

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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, gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD-like / Peptidase C26 / Peptidase C26 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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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)

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