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- PDB-5u55: Psf4 in complex with Mn2+ and (S)-2-HPP -

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Basic information

Entry
Database: PDB / ID: 5u55
TitlePsf4 in complex with Mn2+ and (S)-2-HPP
Components(S)-2-hydroxypropylphosphonic acid epoxidase
KeywordsOXIDOREDUCTASE / Fosfomycin / Epoxidase / Oxidase
Function / homology
Function and homology information


(S)-2-hydroxypropylphosphonic acid epoxidase / dioxygenase activity / antibiotic biosynthetic process / DNA binding / metal ion binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / (S)-2-HYDROXYPROPYLPHOSPHONIC ACID / (S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsChekan, J.R. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)PO1 GM077596 United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Characterization of Two Late-Stage Enzymes Involved in Fosfomycin Biosynthesis in Pseudomonads.
Authors: Olivares, P. / Ulrich, E.C. / Chekan, J.R. / van der Donk, W.A. / Nair, S.K.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: 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_struct_conn_angle / software / struct_conn / struct_ncs_dom_lim
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.value / _software.name / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: (S)-2-hydroxypropylphosphonic acid epoxidase
B: (S)-2-hydroxypropylphosphonic acid epoxidase
C: (S)-2-hydroxypropylphosphonic acid epoxidase
D: (S)-2-hydroxypropylphosphonic acid epoxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,16412
Polymers85,3844
Non-polymers7808
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14570 Å2
ΔGint-96 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.290, 111.005, 128.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRAA5 - 1895 - 189
21TYRTYRBB5 - 1895 - 189
12TYRTYRAA5 - 1895 - 189
22TYRTYRCC5 - 1895 - 189
13TYRTYRAA5 - 1895 - 189
23TYRTYRDD5 - 1895 - 189
14GLYGLYBB5 - 1905 - 190
24GLYGLYCC5 - 1905 - 190
15GLYGLYBB5 - 1905 - 190
25GLYGLYDD5 - 1905 - 190
16GLYGLYCC5 - 1905 - 190
26GLYGLYDD5 - 1905 - 190

NCS ensembles :
ID
6
1
2
3
4
5

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Components

#1: Protein
(S)-2-hydroxypropylphosphonic acid epoxidase / Hydroxypropylphosphonate epoxidase / Ps-hppE


Mass: 21345.881 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: hppE / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JN69, (S)-2-hydroxypropylphosphonic acid epoxidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical
ChemComp-S0H / (S)-2-HYDROXYPROPYLPHOSPHONIC ACID


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


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 20% w/v polyethylene glycol 3350 0.1 M potassium citrate 12 mg/mL Psf4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.45→84.11 Å / Num. obs: 30592 / % possible obs: 100 % / Redundancy: 6.9 % / Net I/σ(I): 18.9
Reflection shellResolution: 2.45→2.46 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.895 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.728 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→84.11 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 10.392 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.609 / ESU R Free: 0.29 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25304 1488 4.9 %RANDOM
Rwork0.20469 ---
obs0.20701 29047 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.271 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2--0.12 Å2-0 Å2
3----3.22 Å2
Refinement stepCycle: 1 / Resolution: 2.45→84.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 36 228 6155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196064
X-RAY DIFFRACTIONr_bond_other_d0.0070.025730
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9498225
X-RAY DIFFRACTIONr_angle_other_deg1.215313106
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6085749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8724.012324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.553151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3841549
X-RAY DIFFRACTIONr_chiral_restr0.0880.2906
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027016
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8714.6322987
X-RAY DIFFRACTIONr_mcbond_other3.874.6322986
X-RAY DIFFRACTIONr_mcangle_it5.9426.9443730
X-RAY DIFFRACTIONr_mcangle_other5.9426.9443731
X-RAY DIFFRACTIONr_scbond_it4.0715.0343077
X-RAY DIFFRACTIONr_scbond_other4.075.0343078
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.497.3764493
X-RAY DIFFRACTIONr_long_range_B_refined9.07836.4236709
X-RAY DIFFRACTIONr_long_range_B_other9.07536.4166667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108030.07
12B108030.07
21A108480.07
22C108480.07
31A106470.09
32D106470.09
41B108810.07
42C108810.07
51B105780.09
52D105780.09
61C105770.09
62D105770.09
LS refinement shellResolution: 2.447→2.511 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 97 -
Rwork0.32 2096 -
obs--100 %

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