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- PDB-1dod: THE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTH... -

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Basic information

Entry
Database: PDB / ID: 1dod
TitleTHE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTHETIC GROUP REGULATES CATALYSIS
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / benzoate catabolic process via hydroxylation / FAD binding / flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...4-hydroxybenzoate 3-monooxygenase / : / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2,4-DIHYDROXYBENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsGatti, D.L. / Palfey, B.A. / Lah, M.S. / Entsch, B. / Massey, V. / Ballou, D.P. / Ludwig, M.L.
Citation
Journal: Science / Year: 1994
Title: The mobile flavin of 4-OH benzoate hydroxylase.
Authors: Gatti, D.L. / Palfey, B.A. / Lah, M.S. / Entsch, B. / Massey, V. / Ballou, D.P. / Ludwig, M.L.
#1: Journal: J.Biol.Chem. / Year: 1976
Title: Flavin-Oxygen Derivatives Involved in Hydroxylation by P-Hydroxybenzoate Hydroxylase
Authors: Entsch, B. / Ballou, D.P. / Massey, V.
History
DepositionSep 6, 1994Processing site: BNL
Revision 1.0Nov 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3223
Polymers44,3831
Non-polymers9402
Water3,045169
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6446
Polymers88,7652
Non-polymers1,8794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6340 Å2
ΔGint-26 kcal/mol
Surface area30380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.900, 146.440, 88.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 275

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Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44382.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / References: UniProt: P20586
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-DOB / 2,4-DIHYDROXYBENZOIC ACID


Mass: 154.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE FLAVIN RING IS PRESENT IN A CONFORMATION DEFINED AS 'OUT' IN WHICH THE FLAVIN HAS MOVED AWAY ...THE FLAVIN RING IS PRESENT IN A CONFORMATION DEFINED AS 'OUT' IN WHICH THE FLAVIN HAS MOVED AWAY FROM THE SUBSTRATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal grow
*PLUS
Temperature: 4-20 ℃ / pH: 7.5 / Method: free interface diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
22 mMp-hydroxybenzoate1drop
30.04 mMFAD1drop
40.3 mMEDTA1drop
530 mMsodium sulphite1drop
60.1 Mphosphate1drop
770 %satammonium sulfate1reservoir
80.1 Mphosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 25883 / % possible obs: 96.64 % / Redundancy: 7.22 % / Rmerge(I) obs: 0.0865

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→15 Å / σ(F): 0
Details: THE HYDROGEN BOND DISTANCE CUTOFF USED FOR THE TURNS IS 3.5 ANGSTROMS. THE CA(X) TO CA(X+4) DISTANCE IS LESS THAN 6.0 ANGSTROMS. THE ANGLES ARE FROM ROBSON AND GARNIER, (1986), 'INTRODUCTION ...Details: THE HYDROGEN BOND DISTANCE CUTOFF USED FOR THE TURNS IS 3.5 ANGSTROMS. THE CA(X) TO CA(X+4) DISTANCE IS LESS THAN 6.0 ANGSTROMS. THE ANGLES ARE FROM ROBSON AND GARNIER, (1986), 'INTRODUCTION TO PROTEINS AND PROTEIN ENGINEERING', ELSEVIER, AMSTERDAM. TYPE PHI2 PSI2 PHI3 PSI3 I -75(+-65) -30(+-40) -90(+-40) -15 TO 40 II -60(+-40) 120(+-40) 90(+-40) 0(+-40) III -75(+-65) -30(+-40) -60(+-40) -15 TO -70 I(PRIME) 75(+-65) 30(+-40) 90(+-40) -40 TO 15 II(PRIME) 60(+-40) -120(+-40) -90(+-40) 0(+-40) III(PRIME) 75(+-65) 30(+-40) 60(+-40) 15 TO 70 RESIDUES 391 - 394 ARE IN A DISORDERED REGION.
RfactorNum. reflection
Rwork0.168 -
obs0.168 25883
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 64 169 3357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection all: 25883 / Rfactor all: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.71

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