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- PDB-5bs5: EPSP synthase from Acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5bs5
TitleEPSP synthase from Acinetobacter baumannii
Components3-phosphoshikimate 1-carboxyvinyltransferaseEPSP synthase
KeywordsTRANSFERASE / Shikimate Pathway / Nucleoside monophosphate (NMP) kinase family / amino acid biosynthesis / ATP-binding / Kinase / nucleotide binding / Synthase
Function / homologyEnolpyruvate transferase domain / Alpha-beta prism / UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain / Alpha Beta / :
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsSutton, K.A. / Schultz, L.W. / Russo, T.A. / Breen, J. / Umland, T.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: EPSP synthase from Acinetobacter baumannii
Authors: Sutton, K.A. / Schultz, L.W. / Russo, T.A. / Breen, J. / Umland, T.C.
History
DepositionJun 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phosphoshikimate 1-carboxyvinyltransferase
B: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)93,7552
Polymers93,7552
Non-polymers00
Water5,909328
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)46,8771
Polymers46,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase


Theoretical massNumber of molelcules
Total (without water)46,8771
Polymers46,8771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.807, 103.896, 113.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid A

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid AB0

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Components

#1: Protein 3-phosphoshikimate 1-carboxyvinyltransferase / EPSP synthase / EPSP synthase


Mass: 46877.328 Da / Num. of mol.: 2 / Fragment: UNP residues 312-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Strain: ATCC 17978 / CIP 53.77 / LMG 1025 / NCDC KC755 / 5377
Gene: A1S_2276 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A3M705, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Bis-Tris Propane, pH 7.0, 0.1M Potassium Bromide, 40% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.49→31.958 Å / Num. obs: 30902 / % possible obs: 99.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 32.25 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.273 / Net I/σ(I): 12.6 / Num. measured all: 134827
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.49-2.574.40.47115251.84596
2.54-2.594.40.43415191.567100
2.59-2.644.40.35715452.78599.4
2.64-2.694.40.35214941.60299.5
2.69-2.754.40.30115481.46999.5
2.75-2.824.40.26415091.0199.8
2.82-2.894.40.22815331.04599.9
2.89-2.964.40.19815591.05299.7
2.96-3.054.40.18815121.34499.7
3.05-3.154.40.16315481.14599.8
3.15-3.264.40.13815191.04499.7
3.26-3.394.40.11915491.08399.9
3.39-3.554.40.09515531.01599.9
3.55-3.734.40.08215431.02199.8
3.73-3.974.30.06915631.02199.9
3.97-4.274.30.05615601.07199.9
4.27-4.74.30.04815681.05799.8
4.7-5.384.30.04715861.13899.9
5.38-6.784.20.04916171.00199.9
6.78-503.90.03216601.11297.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(phenix.refine: 1.9_1682)refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementResolution: 2.49→31.958 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 1556 5.04 %
Rwork0.1722 29346 -
obs0.1749 30902 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.38 Å2 / Biso mean: 41.3601 Å2 / Biso min: 12.23 Å2
Refinement stepCycle: final / Resolution: 2.49→31.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6481 0 0 328 6809
Biso mean---32.63 -
Num. residues----881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046587
X-RAY DIFFRACTIONf_angle_d0.7918900
X-RAY DIFFRACTIONf_chiral_restr0.0311028
X-RAY DIFFRACTIONf_plane_restr0.0041165
X-RAY DIFFRACTIONf_dihedral_angle_d12.5692422
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4940X-RAY DIFFRACTION14.376TORSIONAL
12B4940X-RAY DIFFRACTION14.376TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.57080.29051140.2342564267896
2.5708-2.66260.30491350.242635277099
2.6626-2.76920.28281400.23192617275799
2.7692-2.89520.24681340.210126452779100
2.8952-3.04770.28921420.196726522794100
3.0477-3.23850.25531430.199926592802100
3.2385-3.48820.26471540.191326532807100
3.4882-3.83870.21991300.160426812811100
3.8387-4.3930.17161610.13326982859100
4.393-5.530.18341420.132927202862100
5.53-31.96090.18351610.14092822298399
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)
12.22441.83631.21111.71570.66921.3825-0.10770.2489-0.1864-0.00130.1749-0.2665-0.01750.3663-0.00190.24850.00460.03180.24410.02510.20292.275535.0783-18.9194
22.08150.0831-0.26112.11760.15242.38240.0275-0.1677-0.00020.1497-0.0396-0.00410.10020.21030.02950.198-0.0108-0.00620.21650.00290.1885-2.409510.4668-24.0992
30.48141.25140.4133.09871.15371.22740.0401-0.10790.05510.2527-0.18720.373-0.0393-0.09160.1560.22340.03210.04640.2613-0.02940.2794-9.198929.2692-12.6321
43.0135-0.23051.04242.53330.61672.67010.01430.041-0.15050.28860.0706-0.03810.19360.1651-0.0840.27160.02980.00240.2201-0.02290.21876.480935.988-5.852
51.3385-0.097-0.18982.5648-1.54241.98490.0528-0.19770.06160.4591-0.00170.1543-0.4142-0.1699-0.07420.321-0.0052-0.06170.28640.02560.260137.080926.9704-38.6212
63.09190.9196-0.63081.3117-0.20871.4932-0.0747-0.3122-0.47870.0122-0.0483-0.14750.04480.04440.09230.2330.01650.00240.26070.08410.335129.00922.5811-32.7616
71.46640.6716-1.04613.8922-1.38471.41040.0058-0.1034-0.2956-0.2079-0.2348-0.32790.00540.09580.24730.20690.0135-0.02360.31020.03120.276744.363616.3823-44.2279
82.6239-1.60750.44432.9881-1.11432.89130.24490.3457-0.1927-0.3546-0.10890.4514-0.2573-0.5374-0.10750.36470.0658-0.06240.382-0.00860.363834.39829.9399-51.9689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 312:345 )A312 - 345
2X-RAY DIFFRACTION2( CHAIN A AND RESID 346:517 )A346 - 517
3X-RAY DIFFRACTION3( CHAIN A AND RESID 518:594 )A518 - 594
4X-RAY DIFFRACTION4( CHAIN A AND RESID 595:756 )A595 - 756
5X-RAY DIFFRACTION5( CHAIN B AND RESID 313:344 )B313 - 344
6X-RAY DIFFRACTION6( CHAIN B AND RESID 345:517 )B345 - 517
7X-RAY DIFFRACTION7( CHAIN B AND RESID 518:594 )B518 - 594
8X-RAY DIFFRACTION8( CHAIN B AND RESID 595:756 )B595 - 756

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