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- PDB-3scf: Fe(II)-HppE with S-HPP and NO -

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Basic information

Entry
Database: PDB / ID: 3scf
TitleFe(II)-HppE with S-HPP and NO
ComponentsEpoxidase
KeywordsMETAL BINDING PROTEIN / Cupin-fold / Hydroxypropylphosphonic acid epoxidase / mononuclear non-heme iron enzyme
Function / homology
Function and homology information


(S)-2-hydroxypropylphosphonic acid epoxidase / phosphinothricin biosynthetic process / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / dioxygenase activity / antibiotic biosynthetic process / ferrous iron binding / protein homotetramerization / DNA binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / RmlC-like cupin domain superfamily ...Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / NITRIC OXIDE / (S)-2-HYDROXYPROPYLPHOSPHONIC ACID / (S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDrennan, C.L.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural basis of regiospecificity of a mononuclear iron enzyme in antibiotic fosfomycin biosynthesis.
Authors: Yun, D. / Dey, M. / Higgins, L.J. / Yan, F. / Liu, H.W. / Drennan, C.L.
History
DepositionJun 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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: Epoxidase
B: Epoxidase
C: Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91513
Polymers64,0833
Non-polymers83210
Water48627
1
A: Epoxidase
B: Epoxidase
hetero molecules

A: Epoxidase
B: Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,53218
Polymers85,4454
Non-polymers1,08814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area15650 Å2
ΔGint-156 kcal/mol
Surface area31220 Å2
MethodPISA
2
C: Epoxidase
hetero molecules

C: Epoxidase
hetero molecules

C: Epoxidase
hetero molecules

C: Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,59716
Polymers85,4454
Non-polymers1,15212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area16040 Å2
ΔGint-138 kcal/mol
Surface area30910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.661, 111.661, 152.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Epoxidase


Mass: 21361.127 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces wedmorensis (bacteria) / Gene: fom4 / Plasmid: pPL001 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q56185

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Non-polymers , 5 types, 37 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-S0H / (S)-2-HYDROXYPROPYLPHOSPHONIC ACID


Mass: 140.075 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H9O4P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.7 Å3/Da / Density % sol: 66.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2.0 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 22766 / Num. obs: 22766 / % possible obs: 99.1 % / Redundancy: 10.7 % / Rsym value: 0.101 / Net I/σ(I): 21.9
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.438 / % possible all: 92.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ZZ8

1zz8


Resolution: 2.85→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 1119 random
Rwork0.243 --
all0.269 22379 -
obs0.243 22379 -
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4357 0 43 27 4427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.146
X-RAY DIFFRACTIONc_angle_d0.419

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