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- PDB-1zz9: Crystal Structure of FeII HppE -

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Basic information

Entry
Database: PDB / ID: 1zz9
TitleCrystal Structure of FeII HppE
ComponentsHydroxypropylphosphonic Acid Epoxidase
KeywordsOXIDOREDUCTASE / Mononuclear iron enzyme / Cupin / holo-HppE
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
: / (S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHiggins, L.J. / Yan, F. / Liu, P. / Liu, H.W. / Drennan, C.L.
CitationJournal: Nature / Year: 2005
Title: Structural insight into antibiotic fosfomycin biosynthesis by a mononuclear iron enzyme
Authors: Higgins, L.J. / Yan, F. / Liu, P. / Liu, H.W. / Drennan, C.L.
History
DepositionJun 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

Deposited unit
A: Hydroxypropylphosphonic Acid Epoxidase
B: Hydroxypropylphosphonic Acid Epoxidase
C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5399
Polymers64,0833
Non-polymers4566
Water2,288127
1
A: Hydroxypropylphosphonic Acid Epoxidase
B: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

A: Hydroxypropylphosphonic Acid Epoxidase
B: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,05212
Polymers85,4454
Non-polymers6088
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area13740 Å2
ΔGint-207 kcal/mol
Surface area32590 Å2
MethodPISA, PQS
2
C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5399
Polymers64,0833
Non-polymers4566
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
3
C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules

C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,05212
Polymers85,4454
Non-polymers6088
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
MethodPQS
Unit cell
Length a, b, c (Å)111.870, 111.870, 153.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Hydroxypropylphosphonic Acid 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: pET24b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q56185, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 66.5 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.9791
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 36510 / % possible obs: 94.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.082 / Net I/σ(I): 16.7
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.358 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZZC

1zzc


Resolution: 2.4→15.34 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 872662.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1737 5 %RANDOM
Rwork0.249 ---
obs0.249 34838 90.5 %-
all-36510 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.34 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.73 Å20 Å2
3---1.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→15.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 18 127 4442
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.375 254 5 %
Rwork0.336 4817 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4SO4.PARSO4.TOP

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