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- PDB-3kbr: The crystal structure of cyclohexadienyl dehydratase precursor fr... -

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Basic information

Entry
Database: PDB / ID: 3kbr
TitleThe crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01
ComponentsCyclohexadienyl dehydratase
KeywordsLYASE / cyclohexadienyl dehydratase precursor / Pseudomonas aeruginosa PA01 / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / Multifunctional enzyme / Phenylalanine biosynthesis
Function / homology
Function and homology information


arogenate dehydratase / arogenate dehydratase activity / prephenate dehydratase / prephenate dehydratase activity / L-phenylalanine biosynthetic process / periplasmic space
Similarity search - Function
Cyclohexadienyl dehydratase PheC / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / NICKEL (II) ION / Cyclohexadienyl dehydratase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.659 Å
AuthorsTan, K. / Marshall, N. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01
Authors: Tan, K. / Marshall, N. / Buck, K. / Joachimiak, A.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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.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_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: Cyclohexadienyl dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,52011
Polymers27,6351
Non-polymers88510
Water2,936163
1
A: Cyclohexadienyl dehydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)171,12266
Polymers165,8126
Non-polymers5,31060
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area26010 Å2
ΔGint-68 kcal/mol
Surface area55580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.390, 126.390, 88.981
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
DetailsExperimentally unknown. It is predicted to be monomeric.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cyclohexadienyl dehydratase / Prephenate dehydratase / Arogenate dehydratase


Mass: 27635.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA3475, pheC, Pseudomonas aeruginosa / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037
References: UniProt: Q01269, prephenate dehydratase, arogenate dehydratase

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Non-polymers , 6 types, 173 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005M CoCl2 hexahydrate, 0.005M NiCl2 hexahydrate, 0.005M CaCl2 dihydrate, 0.005M MgCl2 hexahydrate, 0.1M HEPES, 12% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 11, 2009 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.659→28.8 Å / Num. all: 32048 / Num. obs: 32048 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 37.1
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.795 / Mean I/σ(I) obs: 1.75 / % possible all: 93.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.659→28.732 Å / SU ML: 0.21 / σ(F): 1.9 / Phase error: 24.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 3159 5.09 %
Rwork0.1827 --
obs0.1843 62026 98.72 %
all-62026 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.051 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 1.659→28.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 53 163 2071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062010
X-RAY DIFFRACTIONf_angle_d1.0312715
X-RAY DIFFRACTIONf_dihedral_angle_d17.097780
X-RAY DIFFRACTIONf_chiral_restr0.066289
X-RAY DIFFRACTIONf_plane_restr0.004353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6587-1.7180.30613100.29145549X-RAY DIFFRACTION92
1.718-1.78670.32043050.26925861X-RAY DIFFRACTION99
1.7867-1.8680.26993070.2395954X-RAY DIFFRACTION100
1.868-1.96650.24753170.20625976X-RAY DIFFRACTION100
1.9665-2.08970.23343430.195890X-RAY DIFFRACTION100
2.0897-2.2510.1993420.17695959X-RAY DIFFRACTION100
2.251-2.47740.23653020.17345981X-RAY DIFFRACTION100
2.4774-2.83560.22863050.18265959X-RAY DIFFRACTION100
2.8356-3.57150.21573410.17835942X-RAY DIFFRACTION100
3.5715-28.7360.1662870.15875796X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined1.6635-0.26760.0521.74980.21180.98510.00830.09920.058-0.0065-0.0374-0.35890.05180.15110.02590.18110.00770.0350.24520.00450.23627.716817.374236.636
23.96772.31861.00072.2002-0.38122.08790.39240.0103-0.09230.2719-0.1775-0.1313-0.24970.2929-0.17430.3027-0.0791-0.03090.2761-0.02650.3186
Refinement TLS groupSelection details: chain A resid 124:215

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