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- PDB-3g1p: Crystals structure of PhnP from E.coli K-12 -

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Basic information

Entry
Database: PDB / ID: 3g1p
TitleCrystals structure of PhnP from E.coli K-12
ComponentsProtein phnP
KeywordsLYASE / PhnP / C-P lyase / phosphodiesterase / phosphonate utilization / Alkylphosphonate uptake
Function / homology
Function and homology information


phosphoribosyl 1,2-cyclic phosphate phosphodiesterase / phosphoribosyl 1,2-cyclic phosphate phosphodiesterase activity / organic phosphonate catabolic process / manganese ion binding / protein homodimerization activity
Similarity search - Function
Phosphonate metabolism protein PhnP / Phosphonate metabolism protein, MBL domain / : / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / : / Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsPodzelinska, K. / Jia, Z.
CitationJournal: To be Published
Title: Crystals structure of PhnP from E.coli K-12
Authors: Podzelinska, K. / He, S. / Wathier, M. / Yakunin, A. / Proudftoot, M. / Hove-Jensen, B. / Zechel, D. / Jia, Z.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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_ref_seq_dif.details / _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: Protein phnP
B: Protein phnP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,03210
Polymers57,4132
Non-polymers6198
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-40 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.650, 75.405, 83.228
Angle α, β, γ (deg.)90.00, 126.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein phnP


Mass: 28706.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b4092, JW4053, phnP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16692
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MES, Tris, S-Malate, PEG 8000, PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Jun 30, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.4→67.12 Å / Num. obs: 109380 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Rsym value: 8.3 / Net I/σ(I): 31
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 5.5 / Rsym value: 25.7 / % possible all: 64.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoSHARPphasing
REFMAC5.4.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→67 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 0.919 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20982 5171 5 %RANDOM
Rwork0.18583 ---
obs0.18705 98152 94.4 %-
all-98155 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.04 Å2
2---0.51 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.4→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 24 882 4789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0214015
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9525478
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11723.548186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.39715599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.781526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0223152
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8151.52490
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48924018
X-RAY DIFFRACTIONr_scbond_it2.16831525
X-RAY DIFFRACTIONr_scangle_it3.3684.51460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 286 -
Rwork0.224 4965 -
obs--64.91 %

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