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- PDB-5u5d: Psf4 in complex with Mn2+ and (R)-2-HPP -

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Basic information

Entry
Database: PDB / ID: 5u5d
TitlePsf4 in complex with Mn2+ and (R)-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
: / [(2R)-2-hydroxypropyl]phosphonic acid / (S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsChekan, J.R. / Nair, S.K.
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 1.2Mar 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 / 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 / _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)85,96910
Polymers85,3844
Non-polymers5856
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-86 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.464, 111.287, 128.499
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: _ / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA4 - 1904 - 190
21ARGARGBB4 - 1904 - 190
12ARGARGAA4 - 1904 - 190
22ARGARGCC4 - 1904 - 190
13LEULEUAA6 - 1906 - 190
23LEULEUDD6 - 1906 - 190
14ARGARGBB4 - 1904 - 190
24ARGARGCC4 - 1904 - 190
15LEULEUBB6 - 1906 - 190
25LEULEUDD6 - 1906 - 190
16LEULEUCC6 - 1906 - 190
26LEULEUDD6 - 1906 - 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.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TB6 / [(2R)-2-hydroxypropyl]phosphonic 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.: 188 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / Details: 22% PEG 3350 0.2 M Ammonium Citrate 10 mg/mL Psf4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.49→84.12 Å / Num. obs: 28174 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.999 / Rsym value: 0.093 / Net I/σ(I): 20.8
Reflection shellResolution: 2.49→2.498 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.687 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→84.12 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 10.057 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.823 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25003 1363 4.8 %RANDOM
Rwork0.20376 ---
obs0.20605 26750 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.298 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å20 Å2
2--0.79 Å2-0 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.49→84.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5864 0 27 188 6079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196011
X-RAY DIFFRACTIONr_bond_other_d0.0070.025699
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9488144
X-RAY DIFFRACTIONr_angle_other_deg1.401313028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54423.844320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01215997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9671551
X-RAY DIFFRACTIONr_chiral_restr0.0850.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026937
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021468
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_it4.1634.8222963
X-RAY DIFFRACTIONr_mcbond_other4.1634.8222962
X-RAY DIFFRACTIONr_mcangle_it6.5247.2243696
X-RAY DIFFRACTIONr_mcangle_other6.5237.2243697
X-RAY DIFFRACTIONr_scbond_it4.4775.243048
X-RAY DIFFRACTIONr_scbond_other4.4785.2393046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.1627.6784447
X-RAY DIFFRACTIONr_long_range_B_refined10.97837.9726505
X-RAY DIFFRACTIONr_long_range_B_other10.99637.9786471
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)
11A105420.09
12B105420.09
21A99300.13
22C99300.13
31A97290.13
32D97290.13
41B98880.14
42C98880.14
51B95380.13
52D95380.13
61C93430.15
62D93430.15
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 95 -
Rwork0.27 1941 -
obs--99.95 %

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