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- PDB-6wj8: Crystal structure of gamma-aminobutyrate aminotransferase PuuE fr... -

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Basic information

Entry
Database: PDB / ID: 6wj8
TitleCrystal structure of gamma-aminobutyrate aminotransferase PuuE from Klebsiella pneumoniae in complex with PLP
Components4-aminobutyrate aminotransferase PuuE
KeywordsTRANSFERASE / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / 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 ...4-aminobutyrate aminotransferase, bacterial / 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
4-aminobutyrate aminotransferase / 4-aminobutyrate aminotransferase PuuE
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae SA1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsStogios, P.J. / Evdokimova, E. / McChesney, C. / 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: Crystal structure of gamma-aminobutyrate aminotransferase PuuE from Klebsiella pneumoniae in complex with PLP
Authors: Stogios, P.J.
History
DepositionApr 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4-aminobutyrate aminotransferase PuuE
B: 4-aminobutyrate aminotransferase PuuE
C: 4-aminobutyrate aminotransferase PuuE
D: 4-aminobutyrate aminotransferase PuuE


Theoretical massNumber of molelcules
Total (without water)180,7934
Polymers180,7934
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21830 Å2
ΔGint-135 kcal/mol
Surface area49970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.539, 63.351, 128.135
Angle α, β, γ (deg.)90.000, 95.702, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein
4-aminobutyrate aminotransferase PuuE / 4-aminobutyrate--2-oxoglutarate transaminase / Aspartate aminotransferase family protein / Gamma- ...4-aminobutyrate--2-oxoglutarate transaminase / Aspartate aminotransferase family protein / Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase


Mass: 45198.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae SA1 (bacteria)
Gene: puuE, B4U25_33995, BANRA_03059, BL124_00007420, BN49_0292, BVX91_06685, EAO17_12255, EQH49_04735, EQH51_22015, F2X40_16875, F3G17_22490, F3P37_11860, F6W81_01510, FM021_01460, FOB39_08290, ...Gene: puuE, B4U25_33995, BANRA_03059, BL124_00007420, BN49_0292, BVX91_06685, EAO17_12255, EQH49_04735, EQH51_22015, F2X40_16875, F3G17_22490, F3P37_11860, F6W81_01510, FM021_01460, FOB39_08290, NCTC11679_00336, NCTC9617_03808, SAMEA104567806_02818, SAMEA3538476_02828, SK89_04933
Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic
References: UniProt: W9BMV5, UniProt: A0A0H3GYJ5*PLUS, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 43.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 25% PEG3350, 5 mM PLP, GABA. Cryoprotectant 7% gycerol 7% Ethylene glycol 7% Sucrose followed by Paratone followed by annealing in 25% Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→25 Å / Num. obs: 48178 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.18 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.055 / Net I/σ(I): 9.64
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2353 / CC1/2: 0.521 / Rpim(I) all: 0.539 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SF2

1sf2


Resolution: 2.59→24.93 Å / SU ML: 0.3485 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7868
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 1998 4.15 %RANDOM
Rwork0.1955 ---
obs0.1975 48165 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 79.83 Å2
Refinement stepCycle: LAST / Resolution: 2.59→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12674 0 0 178 12852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003812946
X-RAY DIFFRACTIONf_angle_d0.684817610
X-RAY DIFFRACTIONf_chiral_restr0.04711980
X-RAY DIFFRACTIONf_plane_restr0.00452332
X-RAY DIFFRACTIONf_dihedral_angle_d20.7934662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.650.35341290.29763038X-RAY DIFFRACTION90.85
2.65-2.720.31371410.27643249X-RAY DIFFRACTION98.69
2.72-2.80.30541430.26233284X-RAY DIFFRACTION99.13
2.8-2.890.32471410.26193280X-RAY DIFFRACTION99.1
2.89-30.29711440.2453298X-RAY DIFFRACTION99.48
3-3.120.27641410.23293264X-RAY DIFFRACTION99.62
3.12-3.260.27191430.22663291X-RAY DIFFRACTION99.68
3.26-3.430.30151420.22683305X-RAY DIFFRACTION99.88
3.43-3.640.27781450.20063338X-RAY DIFFRACTION99.83
3.64-3.920.23211440.18553321X-RAY DIFFRACTION99.8
3.92-4.320.20661450.16553334X-RAY DIFFRACTION99.91
4.32-4.940.20831450.15233346X-RAY DIFFRACTION99.91
4.94-6.210.24461460.18413384X-RAY DIFFRACTION99.94
6.21-24.930.19521490.17113435X-RAY DIFFRACTION99.53
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)
14.944767124623.95820091908-0.1503647447913.281750511190.6438547560166.2750631983-0.0357095046074-0.317325201209-0.8715512242170.118785110218-0.0411605623629-0.3303412612081.01245907650.4093603922930.06344887141030.7909348992980.08128767635660.05682428075290.3488903489150.0533124612050.5827414851260.84246111774412.519546267138.9385165617
21.408359669340.01110687549760.1952281985990.6444888145580.353046885751.014601878870.02354479672110.06370019263510.106842027602-0.0811934115889-0.0314587608955-0.08112739946450.00404702678698-0.02854325893320.0110372775090.529237451903-0.02041920857680.03978591517230.3120829333910.02963154876050.35965991252-4.4079712644833.037358343624.1497314188
37.814822667150.0360200314953-2.893329673994.78613638564-1.029798927054.01679790371-0.264820177271.00752384347-0.574111675264-0.0385071935615-0.02567509659380.003015172039750.145645985769-0.8556984567620.2936772112660.659358149606-0.0365797778032-0.06413113502820.682915470913-0.06205445386610.401985781966-25.690110337223.66039842549.70088448721
41.605806822050.265558487325-0.2791752627951.437704425010.4574583902870.949187342630.0649908479640.3336288821580.00817474922413-0.294686873145-0.070016501554-0.127918490817-0.182599617811-0.1206929636060.002379391616660.5159483732910.008507248581340.02872662217810.3680937912450.0504439098010.342380607484-9.617728900735.198036393114.9191455006
57.820434704043.664889884462.165989813793.506359265833.766327256455.248943460080.07815071658680.583439775778-0.356846469159-0.03751421058420.273083690459-0.4086026444230.401771724319-0.101732485097-0.3565010977380.49754291363-0.02087456198810.03944008331110.433268634920.01517419798040.3381041161160.23479683943714.29968585225.45953525364
62.51261345386-1.31713126698-0.1391130570374.53108773212-3.048654646498.2165297493-0.311652742385-0.286366025928-0.8000163525660.5770266381110.1485454392820.2160361471570.810976908569-0.62538794737-0.04252624832550.667827761733-0.06499427380850.0553315226160.4248985875550.03134073040530.482215017931-6.406856262496.0406387073515.8954647199
72.234923373710.838141441476-0.9138547647841.74304827159-0.3547432774963.021041153850.08022417927580.0567926506678-0.134718480390.0809976145846-0.03757816041060.01522865781590.3622603161270.0310302440531-0.07515764312280.5389117002820.01045333817950.01027919211330.3091746343690.0166130110930.407261262542.9720909386712.358411337214.9292289014
84.959722076614.700966656515.367432235579.023951958991.462523783318.80915498046-1.024313290560.3322280114980.453600087825-0.9157432209290.479916771237-0.518952004913-1.02365769780.4553532166720.4630886785270.6487895493750.02687064556580.04036756492430.350423185146-0.01642641623140.454346792565-1.9466628168856.232432539624.8504066688
90.828285624437-0.135413357119-0.3723398736160.5907582101330.4601973194970.8261159165190.0394668425452-0.06203546713770.005991238120160.0544104128679-0.0433080701021-0.0523662027795-0.003949710876210.00252699719960.01530530212760.507029380399-0.05901401375550.002610870334950.2788820685010.07061171487990.339727311061-5.8266084928735.453798388639.5727068688
109.79509594944-7.20988097431-0.2143449918945.60862459981-1.073398222827.26999283629-0.399665124263-0.8602923756440.04085219551030.4191470988990.3577757436790.258095254702-0.125643639819-0.494906227070.1072459396530.4641380014240.0004514988626210.05004937093590.4562728353540.029081464680.29853939303-28.848878928842.072404437354.0433207438
110.4575937776780.152932519404-0.3571968048110.787529235445-0.1437878936890.568770488958-0.00149351234583-0.0860558212239-0.02208316159350.2389242638820.00888852925324-0.06155683394070.176784252522-0.0390600280657-0.001369005615080.512375225117-0.024066081067-0.02721822545210.3226275816370.009571183111320.372731027656-9.1373918777135.699118804150.0122009666
126.90724600594-1.91352115809-1.598005742258.479085926133.698721864154.489764003630.270030380715-0.008251665050490.6263408354770.42125431003-0.4023403586260.393286081874-0.697579940136-0.3385477636320.06018889194540.637622959876-0.008537577291910.05631135633580.4393478760280.01146364953230.473131945141-14.542802038958.535122429153.4112198273
139.23995531527-4.37151102915-0.8665534350995.46850930420.4994817180323.488349567430.1408711124410.09851648791970.436225805932-0.219861051998-0.0494209641814-0.0483418178067-0.668299468032-0.123303059213-0.05204021932970.590179684354-0.03860285601570.01777380630760.2942781352030.01082392981840.363700083029-3.2403746024458.895715226947.5564550855
141.78583676986-2.55232918406-1.811112742073.954076905162.916996676782.35122915027-0.380585172967-0.189396369123-0.3055354521810.958337220066-0.1708059636761.096628558220.634098749546-0.4380770907080.5678757613261.00297618254-0.3331013914240.3622872580541.29352390973-0.2280821216751.19316621068-66.312525316121.292591191447.8811494907
151.301734005612.533048886412.463677656296.024601883363.409417789366.605183875830.07987774121911.062066578260.2884241632241.107735244-0.5269681054941.599670059330.257950616864-0.01508822175090.4033585845310.626064529968-0.1284952712360.2041384354531.50566826954-0.3890682598461.14532932738-72.497409152535.937756993635.0133366591
164.78571308165-0.1143836428151.296979467112.05384925966-0.5316492027232.738561968850.1454192450210.4901989099610.0120042989143-0.188895107035-0.2893476048310.5016275928060.131659043003-0.9513142462620.09636788244620.474933290542-0.00926839717282-0.01887666187390.929748128043-0.1445240896760.546233433269-50.335981471239.536931567430.471062445
173.32078209893-3.48199312336-2.370161151524.952821356974.783797412485.81703680056-0.427970238166-0.5082248930350.6179627477320.2716215820750.5410825735810.1668551985560.271676450796-0.470116078774-0.1855517979910.5675117119520.02598136829190.007305166691870.6700260394960.01692974591820.463999729739-36.8272111649.290904951848.6142064415
183.088497622330.418358993082-0.5852527044451.74152405885-0.1163096826592.64152088205-0.0320792344036-0.0005111387239990.12172496920.103704042879-0.2466406091830.434346733485-0.0580080239199-0.7573172123830.2899765200040.4421763345570.0403346439593-0.01580657281320.759878179696-0.1624573338440.639844429615-55.417302593446.666996585540.7473993417
195.423665321880.08400513704544.132650616129.860230335195.181314961677.564807225340.9033611643980.251859259859-0.1347895353361.78713337967-0.0908283389982-0.7152993937472.523387119810.00995690761939-0.7508106142651.426316468530.0321953867916-0.007351176002331.042140064650.008262174251590.820520346303-54.195988733531.730086427164.0561096122
207.374572749710.5280772405620.293553614732.59656387954-0.4516126032573.72219144998-0.07534631166420.129887558592-0.2416203716140.714664320857-0.2096534406260.5750580497150.347447469773-0.3964629662940.2887398916980.814031997594-0.2667922864430.2021576753861.13744814348-0.2299220809380.795469112724-64.734667186237.195125218656.8710256949
211.72429847255-0.068887837574-0.570125312221.664815316080.9721457701130.7613471835720.003661283520310.953715867228-0.501991424925-0.152161970893-0.5463255984760.9780395968310.0188727647262-1.102744825710.4809666267650.707022497147-0.129559557646-0.09242011219381.8421404751-0.4786735410151.23225755602-66.545100219129.183178653121.5626933249
224.646733364230.909562822183-0.82834968562.10587974301-0.4135770097851.964281491150.2193685191460.26573532622-0.3139881392330.207666457907-0.3507191967820.4202994947960.285353402299-0.6215030112920.1111286205670.511824639379-0.1407306984290.005669106048510.702417066686-0.1963739641010.610910266771-43.557262628823.708009512226.5822452783
235.446903218140.5927830921750.09582147014253.10621945142.23079947724.5841040138-0.2466598814570.45812613466-0.0684237408838-0.489559483484-0.5411542414930.7088708238170.146802952188-0.7527147216640.7322465452140.643526932993-0.0832420762868-0.05392130049870.609806555262-0.1780755809490.642113470466-36.789011647515.729724450316.2095501142
241.21400819906-0.543493391175-0.1540698626911.21767241883-0.5360789396440.5218550054560.04931724670210.41581074748-0.721311929895-0.0296649481798-0.4016736411830.776712944070.39570845416-0.8070023842090.2415089826640.731538054811-0.32812651390.05037201465681.204460217-0.484834406381.17347860918-54.550513093513.754417046321.6449652754
254.92918297971-0.384494229763-1.583801919738.49173002798-4.47299421884.982321124850.4523805408650.6252452332140.473549396906-1.55886512285-0.3432669182881.045925462731.18631904978-0.503164413741-0.0380589085181.01638744852-0.00157667571203-0.2108234449861.62828174794-0.4666642024340.917354578314-48.545061626420.4099320192-1.42364507927
263.277486887670.117691649227-1.105375638663.78945805153-1.179431363921.81865557731-0.122828279576-0.008854242335911.17292177238-0.853106385478-0.575055721851.19777085982-0.222218661586-1.016741253390.7119214959511.002125928630.0729724648818-0.2714374426361.96402028501-0.4625271129291.08534303242-60.237931549424.86831151691.26724867478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 164 )
3X-RAY DIFFRACTION3chain 'A' and (resid 165 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 318 )
5X-RAY DIFFRACTION5chain 'A' and (resid 319 through 350 )
6X-RAY DIFFRACTION6chain 'A' and (resid 351 through 380 )
7X-RAY DIFFRACTION7chain 'A' and (resid 381 through 421 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 25 )
9X-RAY DIFFRACTION9chain 'B' and (resid 26 through 168 )
10X-RAY DIFFRACTION10chain 'B' and (resid 169 through 192 )
11X-RAY DIFFRACTION11chain 'B' and (resid 193 through 340 )
12X-RAY DIFFRACTION12chain 'B' and (resid 341 through 367 )
13X-RAY DIFFRACTION13chain 'B' and (resid 368 through 421 )
14X-RAY DIFFRACTION14chain 'C' and (resid 3 through 46 )
15X-RAY DIFFRACTION15chain 'C' and (resid 47 through 70 )
16X-RAY DIFFRACTION16chain 'C' and (resid 71 through 168 )
17X-RAY DIFFRACTION17chain 'C' and (resid 169 through 192 )
18X-RAY DIFFRACTION18chain 'C' and (resid 193 through 357 )
19X-RAY DIFFRACTION19chain 'C' and (resid 358 through 380 )
20X-RAY DIFFRACTION20chain 'C' and (resid 381 through 421 )
21X-RAY DIFFRACTION21chain 'D' and (resid 3 through 95 )
22X-RAY DIFFRACTION22chain 'D' and (resid 96 through 168 )
23X-RAY DIFFRACTION23chain 'D' and (resid 169 through 217 )
24X-RAY DIFFRACTION24chain 'D' and (resid 218 through 340 )
25X-RAY DIFFRACTION25chain 'D' and (resid 341 through 368 )
26X-RAY DIFFRACTION26chain 'D' and (resid 369 through 421 )

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