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- PDB-2h9d: Pyruvate-Bound Structure of the Isochorismate-Pyruvate Lyase from... -

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Basic information

Entry
Database: PDB / ID: 2h9d
TitlePyruvate-Bound Structure of the Isochorismate-Pyruvate Lyase from Pseudomonas aerugionsa
ComponentsSalicylate biosynthesis protein pchB
KeywordsLYASE / intertwined dimer
Function / homology
Function and homology information


pyochelin biosynthetic process / isochorismate lyase / carbon-oxygen lyase activity / isochorismate pyruvate lyase activity / salicylic acid biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity
Similarity search - Function
Salicylate biosynthesis protein PchB / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Salicylate biosynthesis protein PchB / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PYRUVIC ACID / Isochorismate pyruvate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLamb, A.L. / Zaitseva, J. / Lu, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Two Crystal Structures of the Isochorismate Pyruvate Lyase from Pseudomonas aeruginosa.
Authors: Zaitseva, J. / Lu, J. / Olechoski, K.L. / Lamb, A.L.
History
DepositionJun 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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

Downloads & links

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Assembly

Deposited unit
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
C: Salicylate biosynthesis protein pchB
D: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35711
Polymers45,7884
Non-polymers5687
Water3,261181
1
A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0704
Polymers22,8942
Non-polymers1762
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-34 kcal/mol
Surface area9160 Å2
MethodPISA
2
C: Salicylate biosynthesis protein pchB
D: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2867
Polymers22,8942
Non-polymers3925
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-16 kcal/mol
Surface area9590 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14070 Å2
ΔGint-73 kcal/mol
Surface area15840 Å2
MethodPISA
4
C: Salicylate biosynthesis protein pchB
D: Salicylate biosynthesis protein pchB
hetero molecules

A: Salicylate biosynthesis protein pchB
B: Salicylate biosynthesis protein pchB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,35711
Polymers45,7884
Non-polymers5687
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area12590 Å2
ΔGint-62 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.523, 74.636, 88.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains 2 dimers. Each dimer respresents one biological assembly.

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Components

#1: Protein
Salicylate biosynthesis protein pchB / isochorismate-pyruvate lyase


Mass: 11447.064 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PchB / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q51507, Lyases; Carbon-carbon lyases; Other carbon-carbon lyases
#2: Chemical
ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H4O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM ADA, 25% PEG 3350, 0.15 M calcium acetate, 10% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 138 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 22, 2005
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→57.2 Å / Num. obs: 25853 / % possible obs: 95 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.066
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.405 / % possible all: 75.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H9C

2h9c


Resolution: 1.95→57.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2450 -random
Rwork0.21 ---
obs0.21 24992 92.1 %-
all-27138 --
Displacement parametersBiso mean: 28.6 Å2
Refinement stepCycle: LAST / Resolution: 1.95→57.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2980 0 37 181 3198
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0005
X-RAY DIFFRACTIONc_angle_deg1.08

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