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- PDB-5bt8: X-ray Crystal Structure of phosphoglycerate kinase from Acinetoba... -

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Basic information

Entry
Database: PDB / ID: 5bt8
TitleX-ray Crystal Structure of phosphoglycerate kinase from Acinetobacter baumannii
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / phosphoglycerate kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase signature. / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Phosphoglycerate kinase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray Crystal Structure of phosphoglycerate kinase from Acinetobacter baumannii
Authors: Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate kinase
B: Phosphoglycerate kinase
C: Phosphoglycerate kinase
D: Phosphoglycerate kinase
E: Phosphoglycerate kinase
F: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)254,0476
Polymers254,0476
Non-polymers00
Water7,386410
1
A: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phosphoglycerate kinase


Theoretical massNumber of molelcules
Total (without water)42,3411
Polymers42,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.440, 200.290, 87.300
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY IN UNKNOWN

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Components

#1: Protein
Phosphoglycerate kinase /


Mass: 42341.211 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB5075 / Gene: pgk, A591_A2233 / Plasmid: AcbaC.01331.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0A2T205, UniProt: A0A0M3KL68*PLUS, phosphoglycerate kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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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: 2.47 Å3/Da / Density % sol: 50.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MCSG1 screen H9: 0.1 M BIS-TRIS:HCl, pH 5.6, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 106790 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.82 % / Biso Wilson estimate: 33.21 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.085 / Χ2: 0.992 / Net I/σ(I): 14.03 / Num. measured all: 408424
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.360.8530.5462.6130643795279360.63599.8
2.36-2.420.9090.4063.3829776769776950.472100
2.42-2.490.9280.3423.9928740743074270.397100
2.49-2.570.9430.2894.7328116726572620.335100
2.57-2.660.9590.2285.9727227703670340.264100
2.66-2.750.9690.1917.0126391681968160.221100
2.75-2.850.9780.1498.8625276654665450.173100
2.85-2.970.9850.1210.7924438634363410.139100
2.97-3.10.9890.09713.0623448609960980.113100
3.1-3.250.9930.07616.222153579757910.08999.9
3.25-3.430.9950.06618.4720950550355000.07799.9
3.43-3.640.9950.0582119920526652580.06799.8
3.64-3.890.9950.05223.7118458490649000.06199.9
3.89-4.20.9970.04426.6917162457945740.05199.9
4.2-4.60.9980.03829.4815698420241930.04499.8
4.6-5.140.9980.03730.1314313382538190.04399.8
5.14-5.940.9980.03629.4612714336233550.04299.8
5.94-7.270.9980.03331.2110748285828530.03999.8
7.27-10.290.9980.02835.458136220922020.03399.7
10.290.9980.02736.084117124311910.03295.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(dev_2050)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZMR
Resolution: 2.3→48.45 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 2003 1.88 %RANDOM
Rwork0.2151 104727 --
obs0.2157 106730 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.19 Å2 / Biso mean: 40.8111 Å2 / Biso min: 14.14 Å2
Refinement stepCycle: final / Resolution: 2.3→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17028 0 0 410 17438
Biso mean---35.52 -
Num. residues----2376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00417304
X-RAY DIFFRACTIONf_angle_d0.78323616
X-RAY DIFFRACTIONf_chiral_restr0.0382886
X-RAY DIFFRACTIONf_plane_restr0.0033107
X-RAY DIFFRACTIONf_dihedral_angle_d14.01610354
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.35750.3291410.283474947635100
2.3575-2.42130.35231480.274274757623100
2.4213-2.49250.3561380.275874017539100
2.4925-2.5730.35191480.26774807628100
2.573-2.66490.34361470.260274657612100
2.6649-2.77160.2941360.26274847620100
2.7716-2.89770.27591450.253874497594100
2.8977-3.05050.32081350.263775157650100
3.0505-3.24160.28081440.257474877631100
3.2416-3.49180.30681350.23975097644100
3.4918-3.84310.22191470.207374627609100
3.8431-4.39880.1941460.178174997645100
4.3988-5.54080.18371520.157174777629100
5.5408-48.46070.15151410.15097530767199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.1905-0.72210.23963.3479-0.11952.66020.1252-0.0994-0.10110.002-0.20360.37910.3319-0.21980.05490.3211-0.04970.01540.2407-0.0240.2359-1.6312-12.685336.8266
21.75091.9788-0.1484.8620.22380.34070.1373-0.20930.0085-0.0548-0.0905-0.5434-0.04420.0769-0.05640.29840.02420.00640.3126-0.05390.332824.65725.083538.4338
30.5791.0923-0.31234.4028-0.52682.02560.12250.14310.5343-0.54510.0409-0.0531-0.0865-0.0207-0.11310.65210.02160.06410.3504-0.02850.534420.476730.022428.4772
40.63150.21340.04982.58790.33050.3251-0.01120.1122-0.0277-0.85930.0278-0.3361-0.03520.02530.04840.55240.01670.1220.3128-0.05550.330622.41815.320728.0641
53.3851-0.15740.2231.7989-0.83172.2872-0.321-0.1845-0.3261-0.11480.21560.16940.33550.17670.1110.3420.02220.060.2579-0.00950.2136-7.5821-46.277657.1259
63.65280.6215-0.00113.2140.7213.2414-0.11540.0525-0.13-0.17980.0858-0.21970.11610.43840.05830.32770.03140.04770.2631-0.00050.1874-0.342-46.096148.9146
73.3504-2.497-1.20565.07360.84861.10840.14750.3043-0.061-0.3402-0.35320.5891-0.1154-0.16260.07920.3691-0.0897-0.07320.2811-0.02410.2843-20.8132-40.012747.7051
81.68910.54630.24685.13450.33551.944-0.00650.1835-0.0767-0.20290.09740.69120.0252-0.0912-0.05420.1898-0.0099-0.0330.29070.02060.3488-25.5292-9.412351.4067
90.2327-0.0810.19795.07740.26810.124-0.02650.0464-0.04580.40730.12920.53720.0748-0.0467-0.10720.3096-0.01960.06720.3053-0.00470.353-24.6354-23.22258.0203
103.1151.46050.57922.6461-0.64272.479-0.19810.2957-0.221-0.2390.1313-0.0380.24650.10910.01320.2709-0.02690.08280.3075-0.02380.293534.39646.4592-10.1158
112.26241.52750.4432.84770.42980.0678-0.093-0.01810.4511-0.2863-0.02710.2967-0.0633-0.02830.12510.24050.0014-0.00510.2755-0.03380.266326.38987.1186-4.6432
122.5824-0.70890.52326.4750.27012.00050.0926-0.2829-0.2092-0.0543-0.21190.59970.4221-0.1750.09740.27860.0120.01630.281-0.03240.30126.1007-24.931-6.5561
131.61480.95210.04782.492-0.04241.0813-0.03910.04540.2269-0.8464-0.20620.4554-0.13490.00250.24130.37240.0639-0.10680.31440.00950.358611.1437-8.495-14.4614
142.06131.01170.58081.9260.10821.17790.1166-0.27030.1675-0.0311-0.22360.105-0.1417-0.06030.10070.20270.01870.10470.2794-0.03450.2727-34.4097-23.595916.6172
152.145-0.13090.52593.438-0.67341.79150.1103-0.0697-0.0328-0.2026-0.21210.6815-0.0252-0.18590.10460.21020.02580.04050.2619-0.08260.3952-39.7153-23.98927.7308
161.22-1.24680.22261.4245-0.06040.16720.25590.15750.3726-0.6436-0.4083-0.8322-0.01240.19940.01150.36720.09420.150.30180.0610.4998-13.5394-34.51366.4799
171.09780.19870.45311.6168-1.00820.93720.31620.7251-0.1597-1.2193-0.4585-0.85450.58550.5930.43760.71320.43120.39990.58380.13240.5723-7.104-52.35382.7834
181.10120.3685-0.71411.6263-0.12914.38090.28570.5198-0.5895-0.559-0.3721-0.20430.7966-0.04090.05430.47860.09640.00320.35670.01770.5228-14.7967-65.364914.6943
192.0059-1.25420.54550.7877-0.37251.40820.0923-0.34530.50260.3684-0.2755-1.0068-0.21150.45760.0810.22230.0835-0.04570.3860.0780.6089-8.862-48.521717.7431
201.5452-1.25380.49265.8211-1.94130.82940.10710.0397-0.02530.0768-0.3134-0.5392-0.15250.26940.11530.22830.01960.08540.3090.04620.3404-17.2177-34.021511.8695
211.53610.4213-0.06752.02940.42781.99220.03440.01740.0980.0786-0.0219-0.3628-0.04770.19060.00870.1890.0203-0.0420.2101-0.02090.34772.493122.038752.79
222.8254-1.4172-0.07072.51720.10020.99160.05230.3755-0.0503-0.4435-0.18370.5369-0.1874-0.19130.11040.3210.0186-0.05260.2637-0.05870.3424-16.313523.113546.4552
232.1885-0.06140.41721.34181.08661.86180.1450.3907-0.0712-1.0062-0.19290.5869-0.504-0.14570.05590.50370.1456-0.19760.3762-0.04610.4973-28.28547.871742.568
243.3040.1286-1.24962.05020.89133.30810.0995-0.07220.8433-0.11330.003-0.1272-0.9263-0.0744-0.25330.39730.04590.03470.32510.02410.5211-20.573862.483555.8991
250.8467-0.7088-0.092.24030.82040.9280.1126-0.0083-0.0048-0.1206-0.25150.4469-0.1687-0.16280.10710.21260.0172-0.03240.3329-0.0190.4773-24.206440.502754.3391
260.74580.2805-0.05661.87-0.45591.8555-0.4203-0.08060.52920.09740.30640.122-0.2906-0.25180.05760.44830.0198-0.20720.29670.05490.5646-29.739743.973496.5944
273.77260.06321.65951.54440.56226.639-0.2876-0.20840.25-0.19520.13280.7672-0.1091-0.63640.29940.4485-0.0441-0.10030.38490.01040.6035-40.326240.206794.0225
281.35160.30491.75520.29420.17212.4955-0.3434-0.12040.8499-0.2803-0.13070.6003-0.397-0.59630.50920.6321-0.082-0.38610.53550.05760.8569-37.838748.130788.7205
290.79990.57880.18882.4898-0.64511.3853-0.45080.48950.4072-0.38690.2204-0.0669-0.24760.09020.1540.4829-0.1704-0.10730.40730.1130.4296-22.45539.808685.0061
302.15050.05370.78634.8957-1.55623.23940.10850.408-0.0634-0.4025-0.0556-0.09220.03130.4181-0.00760.2263-0.01610.05630.3658-0.06150.3762-11.301110.102789.1548
313.28160.72260.17863.6392-1.06992.28010.0952-0.3407-0.29390.1641-0.1242-0.32480.23970.2726-0.05960.3113-0.00160.01990.2459-0.02580.2953-15.13741.6943100.6765
321.32850.5797-0.04124.1502-0.92240.95190.0171-0.01470.09650.3885-0.0671-0.0851-0.18930.19220.05560.261-0.0524-0.0580.2673-0.00590.2624-12.812323.151199.4539
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:140 )A10 - 140
2X-RAY DIFFRACTION2( CHAIN A AND RESID 141:256 )A141 - 256
3X-RAY DIFFRACTION3( CHAIN A AND RESID 257:291 )A257 - 291
4X-RAY DIFFRACTION4( CHAIN A AND RESID 292:395 )A292 - 395
5X-RAY DIFFRACTION5( CHAIN B AND RESID 7:57 )B7 - 57
6X-RAY DIFFRACTION6( CHAIN B AND RESID 58:140 )B58 - 140
7X-RAY DIFFRACTION7( CHAIN B AND RESID 141:186 )B141 - 186
8X-RAY DIFFRACTION8( CHAIN B AND RESID 187:287 )B187 - 287
9X-RAY DIFFRACTION9( CHAIN B AND RESID 288:395 )B288 - 395
10X-RAY DIFFRACTION10( CHAIN C AND RESID 8:77 )C8 - 77
11X-RAY DIFFRACTION11( CHAIN C AND RESID 78:202 )C78 - 202
12X-RAY DIFFRACTION12( CHAIN C AND RESID 203:294 )C203 - 294
13X-RAY DIFFRACTION13( CHAIN C AND RESID 295:395 )C295 - 395
14X-RAY DIFFRACTION14( CHAIN D AND RESID 9:57 )D9 - 57
15X-RAY DIFFRACTION15( CHAIN D AND RESID 58:160 )D58 - 160
16X-RAY DIFFRACTION16( CHAIN D AND RESID 161:202 )D161 - 202
17X-RAY DIFFRACTION17( CHAIN D AND RESID 203:256 )D203 - 256
18X-RAY DIFFRACTION18( CHAIN D AND RESID 257:294 )D257 - 294
19X-RAY DIFFRACTION19( CHAIN D AND RESID 295:337 )D295 - 337
20X-RAY DIFFRACTION20( CHAIN D AND RESID 338:395 )D338 - 395
21X-RAY DIFFRACTION21( CHAIN E AND RESID 10:140 )E10 - 140
22X-RAY DIFFRACTION22( CHAIN E AND RESID 141:186 )E141 - 186
23X-RAY DIFFRACTION23( CHAIN E AND RESID 187:256 )E187 - 256
24X-RAY DIFFRACTION24( CHAIN E AND RESID 257:284 )E257 - 284
25X-RAY DIFFRACTION25( CHAIN E AND RESID 285:395 )E285 - 395
26X-RAY DIFFRACTION26( CHAIN F AND RESID 7:57 )F7 - 57
27X-RAY DIFFRACTION27( CHAIN F AND RESID 58:92 )F58 - 92
28X-RAY DIFFRACTION28( CHAIN F AND RESID 93:113 )F93 - 113
29X-RAY DIFFRACTION29( CHAIN F AND RESID 114:186 )F114 - 186
30X-RAY DIFFRACTION30( CHAIN F AND RESID 187:243 )F187 - 243
31X-RAY DIFFRACTION31( CHAIN F AND RESID 244:294 )F244 - 294
32X-RAY DIFFRACTION32( CHAIN F AND RESID 295:395 )F295 - 395

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