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- PDB-2phh: THE COENZYME ANALOGUE ADENOSINE 5-DIPHOSPHORIBOSE DISPLACES FAD I... -

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Basic information

Entry
Database: PDB / ID: 2phh
TitleTHE COENZYME ANALOGUE ADENOSINE 5-DIPHOSPHORIBOSE DISPLACES FAD IN THE ACTIVE SITE OF P-HYDROXYBENZOATE HYDROXYLASE. AN X-RAY CRYSTALLOGRAPHIC INVESTIGATION
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
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
ADENOSINE-5-DIPHOSPHORIBOSE / P-HYDROXYBENZOIC ACID / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsVan Derlaan, J.M. / Drenth, J. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1989
Title: The coenzyme analogue adenosine 5-diphosphoribose displaces FAD in the active site of p-hydroxybenzoate hydroxylase. An x-ray crystallographic investigation.
Authors: van der Laan, J.M. / Schreuder, H.A. / Swarte, M.B. / Wierenga, R.K. / Kalk, K.H. / Hol, W.G. / Drenth, J.
#1: Journal: Eur.J.Biochem. / Year: 1989
Title: The Influence of Purification and Protein Heterogeneity on the Crystallization of P-Hydroxybenzoate Hydroxylase
Authors: Van Derlaan, J.M. / Swarte, M.B.A. / Groendijk, H. / Hol, W.G.J. / Drenth, J.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystal Structure of the P-Hydroxylase-Substrate Complex Refined at 1.9 Angstroms Resolution
Authors: Schreuder, H.A. / Prick, P.A.J. / Wierenga, R.K. / Vriend, G. / Wilson, K.S. / Hol, W.G.J. / Drenth, J.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylas Complexed with its Reaction Product 3,4-Dihydroxybenzoate
Authors: Schreuder, H.A. / Van Derlaan, J.M. / Hol, W.G.J. / Drenth, J.
#4: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 1. Completion of the Elucidation of the Primary Structure
Authors: Hofsteenge, J. / Weijer, W.J. / Jekel, P.A. / Beintema, J.J.
#5: Journal: Eur.J.Biochem. / Year: 1983
Title: P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. 2. Fitting of the Amino-Acid Sequence to the Tertiary Structure
Authors: Weijer, W.J. / Hofsteenge, J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#6: Journal: J.Mol.Biol. / Year: 1983
Title: Comparison of the Three-Dimensional Protein and Nucleotide Structure of the Fad-Binding Domain of P-Hydroxybenzoate Hydroxylase with the Fad-as Well as Nadph-Binding Domains of Glutathione Reductase
Authors: Wierenga, R.K. / Drenth, J. / Schulz, G.E.
#7: Journal: Eur.J.Biochem. / Year: 1980
Title: Primary and Tertiary Structure Studies of P-Hydroxybenzoate Hydroxylase from Pseudomonas Fluorescens. Isolation and Alignment of the Cnbr Peptides. Interactions of the Protein with Flavin Adenine Dinucleotide
Authors: Hofsteenge, J. / Vereijken, J.M. / Weijer, W.J. / Beintema, J.J. / Wierenga, R.K. / Drenth, J.
#8: Journal: Eur.J.Biochem. / Year: 1980
Title: The Amino-Acid Sequence of the Three Smallest Cnbr Peptides from P-Hydroxybenzoate Hydroxylase from Pseudomonas Florescens
Authors: Vereijken, J.M. / Hofsteenge, J. / Bak, H.J. / Beintema, J.J.
#9: Journal: J.Mol.Biol. / Year: 1979
Title: Crystal Structure of P-Hydroxybenzoate Hydroxylase
Authors: Wierenga, R.K. / Dejong, R.J. / Kalk, K.H. / Hol, W.G.J. / Drenth, J.
#10: Journal: J.Biol.Chem. / Year: 1975
Title: Crystallization and Preliminary X-Ray Investigation of P-Hydrobenzoate Hydroxylase from Pseudomonas Fluorescens
Authors: Drenth, J. / Hol, W.G.J. / Wierenga, R.K.
History
DepositionJun 19, 1989Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0783
Polymers44,3811
Non-polymers6972
Water1,02757
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1566
Polymers88,7612
Non-polymers1,3954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area5470 Å2
ΔGint-33 kcal/mol
Surface area31210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.700, 146.400, 89.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUE 275 IS A CIS-PROLINE.

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Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44380.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria)
References: UniProt: P00438, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.34 %
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.2 mg/mlenzyme 11
2100 mMpotasssium phosphate11
31 mMenzyme complex(pOHB)11
40.02 mMFAD11
50.15 mMEDTA11
60.10 mMGSH11
760 mMadenosine 5-diphosphoribose11
870 %satammonium sulfate12
9100 mMpotassium phisphate12
101 mMpOHB12
110.02 mMFAD12
120.15 mMEDTA12
130.10 mMGSH12
141.0 M12Na2S2O4

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Data collection

Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 9857 / % possible obs: 70 % / Num. measured all: 19604 / Rmerge(I) obs: 0.066

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.168 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3098 0 46 57 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0350.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0370.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8674
X-RAY DIFFRACTIONp_mcangle_it3.9574
X-RAY DIFFRACTIONp_scbond_it6.7496
X-RAY DIFFRACTIONp_scangle_it8.7739
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.1750.15
X-RAY DIFFRACTIONp_singtor_nbd0.1710.2
X-RAY DIFFRACTIONp_multtor_nbd0.1940.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1860.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 6 Å / Rfactor obs: 0.168 / Num. reflection obs: 8836
Solvent computation
*PLUS
Displacement parameters
*PLUS

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