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- PDB-4ecd: 2.5 Angstrom Resolution Crystal Structure of Bifidobacterium long... -

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Basic information

Entry
Database: PDB / ID: 4ecd
Title2.5 Angstrom Resolution Crystal Structure of Bifidobacterium longum Chorismate Synthase
ComponentsChorismate synthase
KeywordsLYASE / 4-Layer Sandwich / Chorismate synthase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chorismate synthase / chorismate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process
Similarity search - Function
Chorismate synthase signature 3. / Chorismate synthase, AroC fold / Chorismate synthase AroC / Chorismate synthase / Chorismate synthase, conserved site / Chorismate synthase AroC superfamily / Chorismate synthase / Chorismate synthase signature 1. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBifidobacterium longum subsp. infantis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLight, S.H. / Minasov, G. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.5 Angstrom Resolution Crystal Structure of Bifidobacterium longum Chorismate Synthase
Authors: Light, S.H. / Minasov, G. / Krishna, S.N. / Shuvalova, L. / Kwon, K. / Lavie, A. / Anderson, W.F.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate synthase
B: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4326
Polymers85,2912
Non-polymers1424
Water2,396133
1
A: Chorismate synthase
B: Chorismate synthase
hetero molecules

A: Chorismate synthase
B: Chorismate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,86512
Polymers170,5814
Non-polymers2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area9800 Å2
ΔGint-112 kcal/mol
Surface area43290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.944, 123.944, 97.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Chorismate synthase / / 5-enolpyruvylshikimate-3-phosphate phospholyase


Mass: 42645.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum subsp. infantis (bacteria)
Strain: ATCC 15697 / DSM 20088 / JCM 1222 / NCTC 11817 / S12
Gene: aroC, BLIJ_1653, Blon_1598 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: B7GS97, chorismate synthase
#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.: 133 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl (PH 8.3). Screen: 0.2 M Sodium bromide, 0.1 M Bis-tris propane, 20% (w/v) Peg 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 26509 / Num. obs: 26509 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1352 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G85

2g85


Resolution: 2.5→29.54 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.905 / SU B: 15.524 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25347 1312 5 %RANDOM
Rwork0.19702 ---
obs0.19979 25009 97.6 %-
all-25009 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--1.13 Å20 Å2
3----2.25 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3988 0 4 133 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194052
X-RAY DIFFRACTIONr_bond_other_d0.0010.022740
X-RAY DIFFRACTIONr_angle_refined_deg1.6651.9815477
X-RAY DIFFRACTIONr_angle_other_deg0.93836660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0415537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.87423.006163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76115680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8641543
X-RAY DIFFRACTIONr_chiral_restr0.0960.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214547
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02800
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 87 -
Rwork0.278 1670 -
obs--100 %
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)
127.8905-2.462-8.62930.35441.04433.28340.4706-0.5834-0.3872-0.0121-0.149-0.1438-0.0606-0.1548-0.32160.2847-0.0089-0.02690.35380.14960.379220.5886-23.341243.9542
20.67250.03480.23231.12060.77880.79770.0851-0.03790.0432-0.1757-0.10130.0173-0.209-0.14230.01620.3570.03880.01480.22710.03550.197317.3991-15.352434.9294
315.85180.69143.83350.1850.20950.93860.99712.3809-4.5296-0.4939-0.0113-0.20440.0690.5134-0.98581.89310.8885-0.22630.7351-0.67681.295516.9067-33.153710.4856
45.1470.52442.50930.82730.02662.1540.40080.70640.3153-0.4824-0.29870.205-0.13790.0589-0.10210.770.4449-0.00060.50970.0680.106812.7433-23.87813.6636
50.5406-0.0754-0.81280.49990.03191.29240.22160.10440.0082-0.2905-0.1201-0.0828-0.2341-0.1011-0.10160.35350.0837-0.03930.1874-0.00350.246224.3845-30.215325.2667
62.1626-0.461-1.05290.8965-0.32110.8872-0.008-0.05460.0084-0.0760.03250.01840.0537-0.0089-0.02450.33610.03670.01880.2661-0.0020.229925.2275-35.212729.9803
76.7244-9.77729.116314.2725-13.261612.36140.86550.81390.7691-1.6146-1.6169-0.87581.54511.09110.75140.5333-0.40620.1581.3172-0.57251.136830.5643-37.522814.8677
80.44010.4659-0.23481.5120.24370.60030.1506-0.06170.043-0.2699-0.1049-0.1098-0.127-0.0239-0.04570.35050.00120.0720.22560.01770.24729.3492-23.299729.0402
91.75061.1966-0.80371.20510.20262.05630.0955-0.1614-0.0506-0.03320.0031-0.0931-0.11630.1005-0.09860.3027-0.00410.02930.27720.03650.228539.8021-48.205646.4713
101.79020.67162.45030.87541.85416.22340.10720.1083-0.54630.02150.1381-0.23920.35470.5934-0.24530.33540.02870.01490.20410.04260.394142.4245-59.003340.652
110.893-0.24540.5460.50490.1870.60920.034-0.0674-0.1107-0.03540.00180.02250.0181-0.0038-0.03580.3063-0.0130.03130.24110.03560.260134.0523-53.956141.6553
121.2058-0.5606-1.97870.5461.19325.15480.18810.1029-0.3831-0.126-0.11960.1119-0.1064-0.1077-0.06850.34440.0352-0.08440.1593-0.07650.394126.9424-60.340920.7102
130.63830.88120.12431.28530.14210.0665-0.0142-0.0511-0.1161-0.09980.0111-0.0939-0.0195-0.1050.00310.34380.0474-0.0130.22470.00120.269623.9806-48.525132.1631
141.697-0.2502-0.12471.1029-0.02360.0134-0.041-0.097-0.0202-0.17490.04370.0783-0.0114-0.0105-0.00270.30010.0278-0.01440.2432-0.01620.27120.8955-43.022132.2201
151.9924-0.2104-0.91940.02450.15883.5869-0.0063-0.1569-0.2485-0.01090.01520.0363-0.10270.1323-0.00890.31340.01930.03440.2147-0.00420.276129.3515-48.574137.0064
1614.6532-1.04693.38133.80210.35930.9032-0.1472-0.9659-0.50430.11870.31280.1131-0.0153-0.2721-0.16550.1874-0.05330.08040.45520.17850.194718.2297-53.545456.1295
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 10
2X-RAY DIFFRACTION2A11 - 170
3X-RAY DIFFRACTION3A171 - 177
4X-RAY DIFFRACTION4A178 - 210
5X-RAY DIFFRACTION5A211 - 240
6X-RAY DIFFRACTION6A241 - 267
7X-RAY DIFFRACTION7A268 - 296
8X-RAY DIFFRACTION8A297 - 389
9X-RAY DIFFRACTION9B1 - 28
10X-RAY DIFFRACTION10B29 - 64
11X-RAY DIFFRACTION11B65 - 171
12X-RAY DIFFRACTION12B172 - 211
13X-RAY DIFFRACTION13B212 - 238
14X-RAY DIFFRACTION14B239 - 315
15X-RAY DIFFRACTION15B316 - 372
16X-RAY DIFFRACTION16B373 - 389

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