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- PDB-5j6f: Crystal structure of DAH7PS-CM complex from Geobacillus sp. with ... -

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Basic information

Entry
Database: PDB / ID: 5j6f
TitleCrystal structure of DAH7PS-CM complex from Geobacillus sp. with prephenate
Components3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
KeywordsTRANSFERASE / ISOMERASE / tim barrel / dah7ps / dah7p / lyase
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process / metal ion binding
Similarity search - Function
Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA ...Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / PREPHENIC ACID / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
Similarity search - Component
Biological speciesGeobacillus sp. GHH01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsNazmi, A.R. / Othman, M. / Lang, E.J.M. / Bai, Y. / Allison, T.M. / Panjkar, S. / Arcus, V.L. / Parker, E.J.
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Interdomain Conformational Changes Provide Allosteric Regulation en Route to Chorismate.
Authors: Nazmi, A.R. / Lang, E.J.M. / Bai, Y. / Allison, T.M. / Othman, M.H. / Panjikar, S. / Arcus, V.L. / Parker, E.J.
History
DepositionApr 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,81710
Polymers82,8712
Non-polymers9468
Water00
1
A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules

A: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
B: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,63520
Polymers165,7424
Non-polymers1,89316
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area29280 Å2
ΔGint-296 kcal/mol
Surface area47210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.438, 95.438, 167.452
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 3 - 354 / Label seq-ID: 3 - 354

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

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Components

#1: Protein 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase, chorismate mutase-isozyme 3


Mass: 41435.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. GHH01 (bacteria) / Gene: aroA, GHH_c28860 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: L8A208, 3-deoxy-7-phosphoheptulonate synthase, chorismate mutase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PRE / PREPHENIC ACID


Mass: 226.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10O6

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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: 2.66 Å3/Da / Density % sol: 53.7 % / Mosaicity: 0.36 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 ...Details: A protein solution (11 mg/mL in 20 mM BTP, 40 mM KCl, 200 ??M PEP, pH 7.4) was mixed 1:1 (v/v) with a reservoir solution containing 0.2 M sodium citrate, 0.1 M BTP, pH 6.5, 20% W/V PEG 3350 and 0.2 mM chorismic acid. 2 ??L drop size. 500 ??L reservoir volume.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.75→82.65 Å / Num. obs: 22482 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 1 / Rmerge(I) obs: 0.079 / Net I/σ(I): 18
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.75-2.887.71.3361100
9.12-83.737.10.019198.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.1.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TFC

3tfc


Resolution: 2.75→82.65 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 38.682 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 1054 4.7 %RANDOM
Rwork0.18221 ---
obs0.18471 21178 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.759 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å2-0 Å2
2---0.49 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.75→82.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 54 0 5420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195490
X-RAY DIFFRACTIONr_bond_other_d0.0070.025404
X-RAY DIFFRACTIONr_angle_refined_deg2.121.987418
X-RAY DIFFRACTIONr_angle_other_deg1.5112.99912392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67724.549255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84115987
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681543
X-RAY DIFFRACTIONr_chiral_restr0.1070.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026217
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021194
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_it2.7294.6812765
X-RAY DIFFRACTIONr_mcbond_other2.7264.682764
X-RAY DIFFRACTIONr_mcangle_it4.2897.0213451
X-RAY DIFFRACTIONr_mcangle_other4.2897.0223452
X-RAY DIFFRACTIONr_scbond_it3.8955.292725
X-RAY DIFFRACTIONr_scbond_other3.8945.2922726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.267.7463968
X-RAY DIFFRACTIONr_long_range_B_refined7.98137.4586141
X-RAY DIFFRACTIONr_long_range_B_other7.98337.4476140
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 39524 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 75 -
Rwork0.34 1561 -
obs--99.21 %
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)
10.86210.2912-0.51231.7703-1.92725.21790.00460.1040.0358-0.0384-0.13210.2702-0.1823-0.24490.12750.28080.0160.00830.2359-0.12860.2768-50.26128.5123.755
223.4021.7302-2.41253.2927-2.62793.3441-0.7540.3235-1.0869-0.32060.66940.020.9052-0.53910.08460.95880.0379-0.0120.4238-0.20550.6121-30.05216.4731.093
31.8440.4838-0.27220.96720.05251.28310.00160.1211-0.3245-0.2258-0.1014-0.18850.18670.18790.09990.47920.19390.0820.110.0050.1562-12.03329.1590.559
41.2312-0.54120.53343.01351.19631.60370.06690.00480.0912-0.233-0.1058-0.1244-0.25660.2860.03880.2607-0.0918-0.05860.30050.12420.31132.60859.72331.352
5129.05518.7477-22.883311.44660.76524.5756.358-10.662517.35590.3607-3.54253.2382-1.02521.2656-2.81551.6596-0.85550.89592.0642-1.57653.55333.30937.60839.996
61.85361.2275-0.35292.8322-0.21142.11450.2298-0.2843-0.1680.292-0.3882-0.19760.10420.18130.15840.34160.0331-0.03390.15310.09720.183-18.7924.51135.891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 91
2X-RAY DIFFRACTION2A92 - 108
3X-RAY DIFFRACTION3A109 - 354
4X-RAY DIFFRACTION4B1 - 87
5X-RAY DIFFRACTION5B102 - 103
6X-RAY DIFFRACTION6B104 - 354

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