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- PDB-3cht: Crystal Structure of Di-iron AurF with partially bound Ligand -

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Basic information

Entry
Database: PDB / ID: 3cht
TitleCrystal Structure of Di-iron AurF with partially bound Ligand
Componentsp-Aminobenzoate N-Oxygenase
KeywordsOXIDOREDUCTASE / Di-iron oxygenase
Function / homology
Function and homology information


4-aminobenzoate N-oxygenase / oxidoreductase activity / metal ion binding / identical protein binding
Similarity search - Function
: / P-aminobenzoate N-oxygenase AurF / P-aminobenzoate N-oxygenase AurF / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-NITROBENZOIC ACID / MU-OXO-DIIRON / 4-aminobenzoate N-oxygenase
Similarity search - Component
Biological speciesStreptomyces thioluteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, H. / Brunzelle, J.S. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: In vitro reconstitution and crystal structure of p-aminobenzoate N-oxygenase (AurF) involved in aureothin biosynthesis.
Authors: Choi, Y.S. / Zhang, H. / Brunzelle, J.S. / Nair, S.K. / Zhao, H.
History
DepositionMar 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 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

Downloads & links

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Assembly

Deposited unit
A: p-Aminobenzoate N-Oxygenase
B: p-Aminobenzoate N-Oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,6815
Polymers76,2592
Non-polymers4223
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-39.3 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.143, 77.188, 140.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein p-Aminobenzoate N-Oxygenase


Mass: 38129.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thioluteus (bacteria) / Gene: aurF / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q70KH9
#2: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#3: Chemical ChemComp-4NB / 4-NITROBENZOIC ACID / PARA NITROBENZOIC ACID


Mass: 167.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 18-22% PEG 8000, 50 mM Tris-HCl, soaked in 5 mM pNBA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 42156 / Num. obs: 39867 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Redundancy: 4.5 % / Rsym value: 0.075 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4065 / Rsym value: 0.423 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.574 / SU ML: 0.13 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25608 2129 5.1 %RANDOM
Rwork0.20349 ---
obs0.20613 39867 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.711 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å20 Å20 Å2
2--2.42 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 18 230 5040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9676672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1135597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.02522.833240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08515820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6431557
X-RAY DIFFRACTIONr_chiral_restr0.0810.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023763
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.22471
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.23410
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6941.53118
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.10424858
X-RAY DIFFRACTIONr_scbond_it1.7332038
X-RAY DIFFRACTIONr_scangle_it2.7864.51814
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 161 -
Rwork0.237 2755 -
obs--92.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.85690.6842-0.51421.52470.12771.14040.0228-0.24890.45310.1233-0.02520.1642-0.0824-0.02970.0023-0.10880.0297-0.0138-0.2088-0.0032-0.16986.4619-0.3621-4.4721
23.8092-0.4869-1.85511.00460.62683.37830.19120.79260.2297-0.1880.0288-0.0957-0.2529-0.2125-0.22-0.06780.01440.0272-0.0306-0.012-0.130818.1166-11.2298-33.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 33024 - 330
2X-RAY DIFFRACTION2BB24 - 33024 - 330

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