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- PDB-3rp7: Crystal Structure of Klebsiella pneumoniae HpxO complexed with FA... -

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Basic information

Entry
Database: PDB / ID: 3rp7
TitleCrystal Structure of Klebsiella pneumoniae HpxO complexed with FAD and uric acid
Componentsflavoprotein monooxygenase
KeywordsOXIDOREDUCTASE / FAD-binding protein / monooxygenase
Function / homology
Function and homology information


FAD-dependent urate hydroxylase / FAD-dependent urate hydroxylase activity / urate oxidase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / urate catabolic process / purine nucleobase metabolic process / FAD binding
Similarity search - Function
: / D-Amino Acid Oxidase; Chain A, domain 2 - #30 / : / 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 ...: / D-Amino Acid Oxidase; Chain A, domain 2 - #30 / : / 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
FLAVIN-ADENINE DINUCLEOTIDE / URIC ACID / FAD-dependent urate hydroxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.042 Å
AuthorsHicks, K.A. / O'Leary, S.E. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2013
Title: Structural and Mechanistic Studies of HpxO, a Novel Flavin Adenine Dinucleotide-Dependent Urate Oxidase from Klebsiella pneumoniae.
Authors: Hicks, K.A. / O'Leary, S.E. / Begley, T.P. / Ealick, S.E.
History
DepositionApr 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _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: flavoprotein monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3553
Polymers45,4021
Non-polymers9542
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.023, 67.840, 82.236
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein flavoprotein monooxygenase


Mass: 45401.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_16330, KPN_01663 / Plasmid: modified pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A6T923
#2: Chemical ChemComp-URC / URIC ACID / 7,9-DIHYDRO-1H-PURINE-2,6,8(3H)-TRIONE


Mass: 168.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O3
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 291 K / Method: hanging drop
Details: 0.05 M KH2PO4, 20% PEG 8000, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 18, 2009
RadiationMonochromator: Cryo-Cooled Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 24401 / Num. obs: 24401 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.093 / Χ2: 5.912 / Net I/σ(I): 22.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.04-2.115.60.31123831.335199.3
2.11-2.25.60.23823831.231100
2.2-2.35.70.19224141.5691100
2.3-2.425.60.1624281.9111100
2.42-2.575.60.12624192.2951100
2.57-2.775.60.10824043.3471100
2.77-3.055.60.0924544.7331100
3.05-3.495.60.07724418.092199.9
3.49-4.395.40.07248013.56199.5
4.39-5050.068259522.16198.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.042→33.92 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8481 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1229 5.05 %RANDOM
Rwork0.192 ---
obs0.194 24338 99.59 %-
all-24401 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.888 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 63.31 Å2 / Biso mean: 22.8971 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.518 Å20 Å20 Å2
2--1.7806 Å20 Å2
3---1.7374 Å2
Refinement stepCycle: LAST / Resolution: 2.042→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 65 194 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053027
X-RAY DIFFRACTIONf_angle_d1.0354123
X-RAY DIFFRACTIONf_chiral_restr0.068449
X-RAY DIFFRACTIONf_plane_restr0.004532
X-RAY DIFFRACTIONf_dihedral_angle_d12.8991061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.042-2.12380.24681270.19882492261998
2.1238-2.22040.30511260.191725462672100
2.2204-2.33750.22031530.188225162669100
2.3375-2.48390.26811250.193525522677100
2.4839-2.67560.23351350.19725542689100
2.6756-2.94470.25851390.198225712710100
2.9447-3.37050.22831420.191225652707100
3.3705-4.24510.2041330.181226122745100
4.2451-33.92470.2191490.19662701285099

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