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- PDB-5buf: 2.37 Angstrom Structure of EPSP Synthase from acinetobacter baumannii -

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Basic information

Entry
Database: PDB / ID: 5buf
Title2.37 Angstrom Structure of EPSP Synthase from acinetobacter baumannii
Components3-phosphoshikimate 1-carboxyvinyltransferaseEPSP synthase
KeywordsTRANSFERASE / Shikimate pathway / EPSP 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 / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsSutton, K.A. / Schultz, L.W. / Breen, J. / Graham, J. / Umland, T.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States) United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase from the ESKAPE pathogen Acinetobacter baumannii.
Authors: Sutton, K.A. / Breen, J. / Russo, T.A. / Schultz, L.W. / Umland, T.C.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 10, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,8306
Polymers96,6882
Non-polymers1424
Water7,620423
1
A: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4153
Polymers48,3441
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoshikimate 1-carboxyvinyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4153
Polymers48,3441
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.893, 103.380, 113.204
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 B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

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


Mass: 48344.133 Da / Num. of mol.: 2 / Fragment: UNP residues 293-748
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: AB307-0294 / Gene: ABBFA_001168 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA (DE3)
References: UniProt: A0A0A7XPK6, 3-phosphoshikimate 1-carboxyvinyltransferase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 100 mM Bis-Tris propane, pH 7.0, 100 mM potassium bromide, 40% (w/v) PEG 8000
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→34.791 Å / Num. obs: 34793 / % possible obs: 96.89 % / Redundancy: 7.5 % / Rsym value: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.74 / % possible all: 99

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX(phenix.refine: 1.9_1682)refinement
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2o0b

2o0b


Resolution: 2.37→34.791 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1748 5.02 %
Rwork0.1833 33045 -
obs0.1856 34793 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.43 Å2 / Biso mean: 39.5193 Å2 / Biso min: 8.05 Å2
Refinement stepCycle: final / Resolution: 2.37→34.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 4 423 6987
Biso mean--38.97 33.05 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046682
X-RAY DIFFRACTIONf_angle_d0.7989032
X-RAY DIFFRACTIONf_chiral_restr0.031042
X-RAY DIFFRACTIONf_plane_restr0.0031184
X-RAY DIFFRACTIONf_dihedral_angle_d13.1812470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4968X-RAY DIFFRACTION16.542TORSIONAL
12B4968X-RAY DIFFRACTION16.542TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.43950.25181270.21032783291099
2.4395-2.51830.27671580.225227922950100
2.5183-2.60820.27481270.216128242951100
2.6082-2.71260.26471470.213327992946100
2.7126-2.8360.25341620.211328062968100
2.836-2.98550.24061850.213727682953100
2.9855-3.17240.26161360.210228442980100
3.1724-3.41710.27381310.20828372968100
3.4171-3.76070.2441920.20861873196566
3.7607-4.3040.22271660.15592809297599
4.304-5.41930.16931540.13528943048100
5.4193-34.79510.17871630.145830163179100
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)
10.25350.22690.1431.12260.44871.2267-0.0212-0.02170.01390.0576-0.0220.0840.03820.04880.04750.15220.01460.02030.19850.00180.1764-4.029619.9645-19.0983
24.31181.01341.7232.7541-0.1524.78020.2364-0.16-0.81410.1342-0.03410.10820.61470.0408-0.09420.35720.0128-0.02630.20850.04110.3114.426828.03-0.6811
31.9733-0.25021.03532.1206-0.12563.3862-0.0140.0907-0.01460.03680.0959-0.2261-0.02750.4062-0.09230.2262-0.0101-0.00350.2341-0.04190.246111.952537.9259-7.5279
42.55310.2692-0.32292.1257-0.95341.5053-0.0624-0.24740.14770.3250.18090.1101-0.3343-0.2052-0.03550.29570.0412-0.03430.3163-0.00630.184636.397826.689-38.7723
53.63970.655-0.59351.1062-0.01291.2752-0.2193-0.3207-0.8125-0.025-0.0114-0.2230.10150.12370.17120.25310.05010.05280.28150.13430.404530.64661.7883-33.4863
62.8946-0.5652-0.66252.2762-1.11712.18870.0830.2592-0.209-0.0793-0.1088-0.01480.05790.18750.09170.2040-0.01750.2832-0.02480.237445.176922.9579-48.9712
73.7464-1.64020.35392.33460.27054.83690.3990.9931-0.382-0.5102-0.38540.3893-0.0376-0.9459-0.0560.34240.1268-0.08760.6304-0.08760.326931.630429.4469-59.7143
84.1668-0.6044-0.4414.4345-0.53394.0327-0.0555-0.1848-0.15050.31620.19360.43-0.3229-0.5491-0.07650.30350.10480.02730.33580.03540.259229.921134.3452-43.7508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 312:621 )A312 - 621
2X-RAY DIFFRACTION2( CHAIN A AND RESID 622:660 )A622 - 660
3X-RAY DIFFRACTION3( CHAIN A AND RESID 661:756 )A661 - 756
4X-RAY DIFFRACTION4( CHAIN B AND RESID 312:344 )B312 - 344
5X-RAY DIFFRACTION5( CHAIN B AND RESID 345:540 )B345 - 540
6X-RAY DIFFRACTION6( CHAIN B AND RESID 541:631 )B541 - 631
7X-RAY DIFFRACTION7( CHAIN B AND RESID 632:700 )B632 - 700
8X-RAY DIFFRACTION8( CHAIN B AND RESID 701:756 )B701 - 756

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