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- PDB-6al9: Crystal structure of chorismate mutase from Helicobacter pylori i... -

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Basic information

Entry
Database: PDB / ID: 6al9
TitleCrystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate
ComponentsChorismate mutase
KeywordsISOMERASE / Chorismic acid / Catalysis / Helicobacter pylori / Ligands / Chorismate mutase / Prephenate
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Chorismate mutase / Chorismate mutase domain superfamily / Chorismate Mutase Domain, subunit A / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
P-HYDROXYBENZOIC ACID / PREPHENIC ACID / PYRUVIC ACID / Chorismate mutase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFan, Y. / Jameson, G.B. / Panjikar, S. / Parker, E.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
MarsdenUOC1105 New Zealand
CitationJournal: To Be Published
Title: Crystal structure of chorismate mutase from Helicobacter pylori in complex with prephenate
Authors: Fan, Y. / Jameson, G.B. / Panjikar, S. / Parker, E.J.
History
DepositionAug 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,1535
Polymers22,7002
Non-polymers4523
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.869, 63.526, 166.918
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 6 - 94 / Label seq-ID: 6 - 94

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.964193, -0.195856, 0.178807), (-0.195399, 0.068797, -0.978308), (0.179306, -0.978216, -0.104604)-38.96278, 16.03653, 25.24441

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Components

#1: Protein Chorismate mutase /


Mass: 11350.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: HP_0291 / Production host: Escherichia coli (E. coli) / References: UniProt: O25064
#2: Chemical ChemComp-PRE / PREPHENIC ACID / Prephenic acid


Mass: 226.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H10O6
#3: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID / 4-Hydroxybenzoic acid


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES pH 6.5, 0.2 M ammonium acetate, 35% glycerol ethoxylate, 0.5 mM chorismate acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2015
RadiationMonochromator: DOUBLE CRYSTAL SI (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→41.73 Å / Num. obs: 10877 / % possible obs: 99.1 % / Redundancy: 8.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Net I/σ(I): 11.6
Reflection shellResolution: 2.21→2.28 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 4.1 / CC1/2: 0.911 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YBZ, 2D8D and 3RMI

1ybz

2d8d

3rmi


Resolution: 2.3→19.43 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 15.681 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.347 / ESU R Free: 0.228
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE DENSITY IN THE ACTIVE SITE IN CHAIN B IS UNEQUIVOCALLY INCONSISTENT WITH PREPHENATE (PRE) AND IS WELL FITTED BY PARAHYDROXYBENZOATE (PHB) ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE DENSITY IN THE ACTIVE SITE IN CHAIN B IS UNEQUIVOCALLY INCONSISTENT WITH PREPHENATE (PRE) AND IS WELL FITTED BY PARAHYDROXYBENZOATE (PHB) AND PYRUVATE (PYR). THE DENSITY IN THE ACTIVE SITE OF CHAIN A IS CONSISTENT WITH PREPHENATE (PHE)
RfactorNum. reflection% reflectionSelection details
Rfree0.23691 464 4.9 %RANDOM
Rwork0.20611 ---
obs0.2076 9097 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å2-0 Å2
2--0.55 Å20 Å2
3----0.32 Å2
Refinement stepCycle: 1 / Resolution: 2.3→19.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 32 13 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191535
X-RAY DIFFRACTIONr_bond_other_d00.021553
X-RAY DIFFRACTIONr_angle_refined_deg1.3012.032054
X-RAY DIFFRACTIONr_angle_other_deg3.4133579
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24624.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.03415321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.4011512
X-RAY DIFFRACTIONr_chiral_restr0.3290.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021685
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02331
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_it2.5222.711722
X-RAY DIFFRACTIONr_mcbond_other2.5232.707721
X-RAY DIFFRACTIONr_mcangle_it3.8944.045899
X-RAY DIFFRACTIONr_mcangle_other3.8924.05900
X-RAY DIFFRACTIONr_scbond_it3.4123.138813
X-RAY DIFFRACTIONr_scbond_other3.413.141814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5694.5471156
X-RAY DIFFRACTIONr_long_range_B_refined7.39431.7561699
X-RAY DIFFRACTIONr_long_range_B_other7.39231.7571700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5300 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 32 -
Rwork0.214 651 -
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)
10.0667-0.0456-0.24742.12050.81911.8758-0.01850.0099-0.0419-0.2565-0.0180.0296-0.1008-0.03880.03650.048-0.01810.02760.0631-0.03630.0585-19.8226-5.13317.2265
20.17720.2679-0.37262.81090.70251.47120.0417-0.0056-0.0148-0.0192-0.0328-0.0917-0.1293-0.025-0.00890.0207-0.02450.01330.0828-0.04870.0537-15.7812.00624.6542
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 95
2X-RAY DIFFRACTION2B5 - 95

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