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- PDB-1bjp: CRYSTAL STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE INACTIVATED BY ... -

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Basic information

Entry
Database: PDB / ID: 1bjp
TitleCRYSTAL STRUCTURE OF 4-OXALOCROTONATE TAUTOMERASE INACTIVATED BY 2-OXO-3-PENTYNOATE AT 2.4 ANGSTROMS RESOLUTION
Components4-OXALOCROTONATE TAUTOMERASE
KeywordsISOMERASE / TAUTOMERASE / MICROBIAL BIODEGRADATION
Function / homology
Function and homology information


xylene catabolic process / 2-hydroxymuconate tautomerase / toluene catabolic process / isomerase activity
Similarity search - Function
4-oxalocrotonate tautomerase, Pseudomonas-type / 4-oxalocrotonate tautomerase / Tautomerase enzyme / Macrophage Migration Inhibitory Factor / Macrophage Migration Inhibitory Factor / Tautomerase/MIF superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-OXO-3-PENTENOIC ACID / 2-hydroxymuconate tautomerase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTaylor, A.B. / Czerwinski, R.M. / Johnson Junior, W.H. / Whitman, C.P. / Hackert, M.L.
CitationJournal: Biochemistry / Year: 1998
Title: Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 A resolution: analysis and implications for the mechanism of inactivation and catalysis.
Authors: Taylor, A.B. / Czerwinski, R.M. / Johnson Jr., W.H. / Whitman, C.P. / Hackert, M.L.
History
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Dec 2, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68010
Polymers34,1095
Non-polymers5705
Water1,40578
1
A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

A: 4-OXALOCROTONATE TAUTOMERASE
B: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,61612
Polymers40,9316
Non-polymers6856
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14750 Å2
ΔGint-25 kcal/mol
Surface area14780 Å2
MethodPISA, PQS
2
C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules

C: 4-OXALOCROTONATE TAUTOMERASE
D: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,61612
Polymers40,9316
Non-polymers6856
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14630 Å2
ΔGint-32 kcal/mol
Surface area13250 Å2
MethodPISA, PQS
3
E: 4-OXALOCROTONATE TAUTOMERASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)41,61612
Polymers40,9316
Non-polymers6856
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_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area14780 Å2
ΔGint-25 kcal/mol
Surface area14700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.700, 78.700, 314.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
4-OXALOCROTONATE TAUTOMERASE / 4-OXALOCROTONATE ISOMERASE


Mass: 6821.838 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: MT-2 / Gene: XYLH / Plasmid: PBAOT1 / Gene (production host): XYLH / Production host: Escherichia coli (E. coli) / Strain (production host): S606
References: UniProt: Q01468, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups
#2: Chemical
ChemComp-OXP / 2-OXO-3-PENTENOIC ACID


Mass: 114.099 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
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: 2.8 Å3/Da / Density % sol: 55 %
Description: PDB ENTRY 1OTF WAS USED TO SOLVE THE STARTING MOLECULAR REPLACEMENT MODEL
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, sitting drop
Details: 5 microlitter of drop solution was mixed with 5 microlitter precipitant
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
250 mMsodium phosphate1drop
314 %PEG80001reservoirprecipitant
450 mMsodium phosphate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MSC MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→24 Å / Num. obs: 15183 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.148 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.354 / % possible all: 100
Reflection
*PLUS
Num. measured all: 248309 / Rmerge(I) obs: 0.156

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2.3 ANGSTROM RESOLUTION STRUCTURE OF NATIVE 4-OXALOCROTONATE TAUTOMERASE FROM PSEUDOMONAS PUTIDA MT-2

Resolution: 2.4→24 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 728 5 %RANDOM
Rwork0.206 ---
obs0.206 14606 96.2 %-
Displacement parametersBiso mean: 26.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-24 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 40 78 2446
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.171.5
X-RAY DIFFRACTIONx_mcangle_it3.252
X-RAY DIFFRACTIONx_scbond_it4.482
X-RAY DIFFRACTIONx_scangle_it7.132.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 1.5 / Weight position: 200

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINED5.230.14
2216.340.12
3319.140.25
447.920.14
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.347 59 4.4 %
Rwork0.238 1271 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION22O3P.PAR2O3P.TOP
X-RAY DIFFRACTION3TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor obs: 0.238

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