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- PDB-1zz8: Crystal Structure of FeII HppE in Complex with Substrate Form 2 -

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Basic information

Entry
Database: PDB / ID: 1zz8
TitleCrystal Structure of FeII HppE in Complex with Substrate Form 2
ComponentsHydroxypropylphosphonic Acid Epoxidase
KeywordsOXIDOREDUCTASE / Substrate-Enzyme Complex / Cupin / Mononuclear 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 transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...: / Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / 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 / (S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesStreptomyces wedmorensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID BODY REFINEMENT / Resolution: 2.3 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Hydroxypropylphosphonic Acid Epoxidase
B: Hydroxypropylphosphonic Acid Epoxidase
C: Hydroxypropylphosphonic Acid Epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6719
Polymers64,0833
Non-polymers5886
Water2,630146
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)86,22812
Polymers85,4454
Non-polymers7848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area14670 Å2
ΔGint-154 kcal/mol
Surface area31320 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)64,6719
Polymers64,0833
Non-polymers5886
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area14970 Å2
ΔGint-146 kcal/mol
Surface area30960 Å2
MethodPISA
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)86,22812
Polymers85,4454
Non-polymers7848
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)111.649, 111.649, 152.069
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-S0H / (S)-2-HYDROXYPROPYLPHOSPHONIC ACID


Mass: 140.075 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H9O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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 %
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1271
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 42988 / % possible obs: 99.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 6.8 / Rsym value: 0.218 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: RIGID BODY REFINEMENT
Starting model: PDB ENTRY 1ZZ9

1zz9


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 443915.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1852 4.4 %RANDOM
Rwork0.225 ---
obs0.225 41747 96.3 %-
all-42988 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.55 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 36.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å20 Å20 Å2
2---4.42 Å20 Å2
3---8.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 27 146 4515
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 77 1.2 %
Rwork0.274 6450 -
obs--92 %
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 DIFFRACTION4S_HPP.PARAMS_HPP.TOP

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