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- PDB-7rca: Crystal structure of Aro2p chorismate synthase from Candida lusitaniae -

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Basic information

Entry
Database: PDB / ID: 7rca
TitleCrystal structure of Aro2p chorismate synthase from Candida lusitaniae
ComponentsChorismate synthase
KeywordsLYASE / Candida / chorimsate / 5-O-(1-carboxyvinyl)-3-phosphoshikimate / alpha/beta protein / Structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase signature 2. / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1.
Similarity search - Domain/homology
Biological speciesClavispora lusitaniae (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsStogios, P.J. / Evdokimova, E. / 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 Aro2p chorismate synthase from Candida lusitaniae
Authors: Stogios, P.J.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1144
Polymers40,9471
Non-polymers1673
Water2,792155
1
A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules

A: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,45616
Polymers163,7884
Non-polymers66812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area27820 Å2
ΔGint-268 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.086, 94.086, 84.618
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-403-

CL

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Components

#1: Protein Chorismate synthase


Mass: 40947.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clavispora lusitaniae (fungus) / Gene: Aro2 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: A0A202G8T3, chorismate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.1 M NaCl, 0.1 M HEPES pH 7.2, 1.6 M ammonium sulfate

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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: Oct 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. obs: 17965 / % possible obs: 98.2 % / Redundancy: 13.7 % / Biso Wilson estimate: 44.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.023 / Net I/σ(I): 29.8
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 9.9 % / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 726 / CC1/2: 0.798 / Rpim(I) all: 0.357 / % possible all: 80.2

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1r53

1r53


Resolution: 2.26→29.83 Å / SU ML: 0.2822 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.1785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2529 1693 10.02 %RANDOM
Rwork0.1997 15195 --
obs0.205 16888 92.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.96 Å2
Refinement stepCycle: LAST / Resolution: 2.26→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 7 155 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312814
X-RAY DIFFRACTIONf_angle_d0.59973800
X-RAY DIFFRACTIONf_chiral_restr0.0453419
X-RAY DIFFRACTIONf_plane_restr0.0046507
X-RAY DIFFRACTIONf_dihedral_angle_d23.77811067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.330.3188930.2734897X-RAY DIFFRACTION66.4
2.33-2.410.30911270.25361091X-RAY DIFFRACTION82.13
2.41-2.490.31521300.24391216X-RAY DIFFRACTION89.79
2.49-2.590.30131410.24631202X-RAY DIFFRACTION90.44
2.59-2.710.30811390.24691250X-RAY DIFFRACTION92.79
2.71-2.850.31581440.23541295X-RAY DIFFRACTION95.61
2.85-3.030.28691470.23211323X-RAY DIFFRACTION96.46
3.03-3.260.30831450.22341319X-RAY DIFFRACTION97.41
3.26-3.590.25731510.19121354X-RAY DIFFRACTION98.95
3.59-4.110.21981530.16491362X-RAY DIFFRACTION98.7
4.11-5.170.20921550.16071399X-RAY DIFFRACTION99.87
5.18-29.830.23011680.20091487X-RAY DIFFRACTION99.34
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)
19.27651040416-2.33213358494-2.648286770178.163365129441.317899872293.25312331265-0.06836172637780.9061440106090.206849655018-0.7520533124730.0196376643124-0.2651993154870.0239010408075-0.0539321976860.2748688926610.3155656192190.0245198882934-0.02911462289710.3254957526150.003887861054260.4447866578313.37874840475.34935893845-1.26820562485
20.55771409845-0.8305253162981.167590431374.67452440964-1.954772454317.742795640970.03575966646380.03385698133220.144416605080.0911211180322-0.17677309625-0.692175250353-0.3015680948780.6538561591170.07987740014410.3343340896-0.0667295282874-0.1000226746890.3579018230440.00414383448920.57681367784622.65802237269.740089656688.81479208885
36.42403338511-2.72139827254-2.940402159154.084767998491.449055526073.291565792640.0954195195240.4283024532640.27641850956-0.4448072027750.0182599751283-0.185342246122-0.3892589563290.475405112979-0.082939232620.379066653862-0.0397169458404-0.06921544060760.457622636866-0.03850610957840.48868551038319.099001675913.91136550614.14054376083
41.61121961199-0.1859740234030.6933843194611.340735919940.04577938908171.53996245830.00752441569630.0527159840297-0.0256616526496-0.034147191834-0.0384476269513-0.3281757146680.02936433610660.441005906780.04162880511130.3382252732870.0185457897732-0.007584262905330.3770608698430.0336849931640.51357600658526.4919601691-8.259112624083.59525493171
53.155245605591.20565511996-2.393283986124.23310257839-3.012088130335.53211797197-0.0602906305999-0.673504972168-0.2378540956360.460064857360.0405497101796-0.2160661538170.1493934973130.3564271560370.01600602467020.3540923449820.0484902974226-0.1063820053550.4334590976960.04980663224830.47085452445115.6111917027-20.202232996112.9551593284
62.12847895672-0.655999112621-1.106383550351.447051491310.8774136097161.66195937854-0.01289943875530.06511746782290.00679446356-0.161962687540.0183017867745-0.335866449307-0.06724070463060.177877123259-0.06508374495930.3660472085260.0135857116555-0.03881645032710.3557550455070.04436248171930.46216603028820.1347813929-7.288266436940.969352605564
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -1 through 19 )-1 - 191 - 21
22chain 'A' and (resid 20 through 65 )20 - 6522 - 58
33chain 'A' and (resid 66 through 96 )66 - 9659 - 83
44chain 'A' and (resid 97 through 237 )97 - 23784 - 224
55chain 'A' and (resid 238 through 291 )238 - 291225 - 278
66chain 'A' and (resid 292 through 376 )292 - 376279 - 363

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