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- PDB-4bps: Crystal structure of Chorismatase at 1.08 Angstrom resolution. -

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Basic information

Entry
Database: PDB / ID: 4bps
TitleCrystal structure of Chorismatase at 1.08 Angstrom resolution.
ComponentsFKBO
KeywordsHYDROLASE / YJGF FOLD
Function / homologychorismatase / Chorismatase, FkbO/Hyg5 family / ether hydrolase activity / RutC-like superfamily / : / 3-(2-CARBOXYETHYL)BENZOIC ACID / Chorismatase
Function and homology information
Biological speciesSTREPTOMYCES HYGROSCOPICUS SUBSP. ASCOMYCETICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.081 Å
AuthorsJuneja, P. / Hubrich, F. / Diederichs, K. / Welte, W. / Andexer, J.N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Mechanistic Implications for the Chorismatase Fkbo Based on the Crystal Structure.
Authors: Juneja, P. / Hubrich, F. / Diederichs, K. / Welte, W. / Andexer, J.N.
History
DepositionMay 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Atomic model / Database references / Other
Revision 1.3Jun 29, 2016Group: Structure summary
Revision 1.4May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FKBO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4212
Polymers37,2271
Non-polymers1941
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.139, 52.250, 52.532
Angle α, β, γ (deg.)90.00, 93.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FKBO / CHORISMATASE


Mass: 37226.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES HYGROSCOPICUS SUBSP. ASCOMYCETICUS (bacteria)
Plasmid: PET28A-FKBO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RP-PL1SL2 / References: UniProt: Q9KID9
#2: Chemical ChemComp-3EB / 3-(2-CARBOXYETHYL)BENZOIC ACID


Mass: 194.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 1.81 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES PH6.5, 20-23% PEG 4000, HANGING DROP, VAPOUR DIFFUSION, 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97794
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 5, 2013 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.08→37.01 Å / Num. obs: 103504 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 3.09 % / Biso Wilson estimate: 6.95 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 1.85 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.77 / % possible all: 47.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1358)refinement
XDSdata reduction
XDSphasing
HKL2MAPphasing
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.081→37.014 Å / SU ML: 0.07 / σ(F): 1.11 / Phase error: 13.57 / Stereochemistry target values: ML
Details: RESIDUE 28-33, HAVE LOW ELECTRON DENSITY, RESIDUE 33 GLU SIDE CHAIN IS NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.1465 8867 5 %
Rwork0.1264 --
obs0.1274 103501 79.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 11.7 Å2
Refinement stepCycle: LAST / Resolution: 1.081→37.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 14 611 3126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012631
X-RAY DIFFRACTIONf_angle_d1.4483605
X-RAY DIFFRACTIONf_dihedral_angle_d12.246955
X-RAY DIFFRACTIONf_chiral_restr0.088413
X-RAY DIFFRACTIONf_plane_restr0.008486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0808-1.09310.3021640.22071349X-RAY DIFFRACTION19
1.0931-1.1060.2171340.20822726X-RAY DIFFRACTION39
1.106-1.11940.17941680.18623113X-RAY DIFFRACTION44
1.1194-1.13360.17831880.17033671X-RAY DIFFRACTION52
1.1336-1.14850.16621930.15874151X-RAY DIFFRACTION58
1.1485-1.16430.17872570.15184645X-RAY DIFFRACTION65
1.1643-1.18090.15522840.15055077X-RAY DIFFRACTION73
1.1809-1.19850.17793300.1525755X-RAY DIFFRACTION81
1.1985-1.21730.16053420.13885912X-RAY DIFFRACTION84
1.2173-1.23720.17162990.13946033X-RAY DIFFRACTION85
1.2372-1.25860.16213550.13976061X-RAY DIFFRACTION85
1.2586-1.28140.1633320.13486046X-RAY DIFFRACTION86
1.2814-1.30610.15743050.13375948X-RAY DIFFRACTION85
1.3061-1.33280.15533060.12896044X-RAY DIFFRACTION85
1.3328-1.36170.15643560.12396232X-RAY DIFFRACTION88
1.3617-1.39340.15573400.12216244X-RAY DIFFRACTION88
1.3934-1.42830.15743310.11876222X-RAY DIFFRACTION89
1.4283-1.46690.15353430.11146220X-RAY DIFFRACTION89
1.4669-1.510.13473410.10716265X-RAY DIFFRACTION88
1.51-1.55880.13823070.10766200X-RAY DIFFRACTION88
1.5588-1.61450.14323320.10716430X-RAY DIFFRACTION91
1.6145-1.67910.13463080.10856482X-RAY DIFFRACTION91
1.6791-1.75560.12013380.11516510X-RAY DIFFRACTION92
1.7556-1.84810.14413550.11866450X-RAY DIFFRACTION92
1.8481-1.96390.12542940.12226417X-RAY DIFFRACTION90
1.9639-2.11550.12083280.11426729X-RAY DIFFRACTION94
2.1155-2.32840.14193760.12186604X-RAY DIFFRACTION94
2.3284-2.66520.15413160.13266571X-RAY DIFFRACTION93
2.6652-3.35750.13863140.12946665X-RAY DIFFRACTION94
3.3575-37.03590.14493310.12786571X-RAY DIFFRACTION93

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