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- PDB-4mln: Crystal of PhnZ bound to (R)-2-amino-1-hydroxyethylphosphonic acid -

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Basic information

Entry
Database: PDB / ID: 4mln
TitleCrystal of PhnZ bound to (R)-2-amino-1-hydroxyethylphosphonic acid
ComponentsPredicted HD phosphohydrolase PhnZ
KeywordsHYDROLASE / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / all alpha / Carbon-phosphorus bond cleavage
Function / homology
Function and homology information


2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming) / oxidoreductase activity / hydrolase activity / metal ion binding
Similarity search - Function
HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / HD domain / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / [(1R)-2-amino-1-hydroxyethyl]phosphonic acid / 2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming)
Similarity search - Component
Biological speciesuncultured bacterium HF130_AEPn_1 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
Authorsvan Staalduinen, L.M. / McSorley, F.R. / Zechel, D.L. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of PhnZ in complex with substrate reveals a di-iron oxygenase mechanism for catabolism of organophosphonates.
Authors: van Staalduinen, L.M. / McSorley, F.R. / Schiessl, K. / Seguin, J. / Wyatt, P.B. / Hammerschmidt, F. / Zechel, D.L. / Jia, Z.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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

Downloads & links

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Assembly

Deposited unit
A: Predicted HD phosphohydrolase PhnZ
B: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3988
Polymers44,8922
Non-polymers5066
Water2,486138
1
A: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6994
Polymers22,4461
Non-polymers2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Predicted HD phosphohydrolase PhnZ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6994
Polymers22,4461
Non-polymers2533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.630, 74.910, 75.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Predicted HD phosphohydrolase PhnZ


Mass: 22446.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium HF130_AEPn_1 (environmental samples)
Gene: ALOHA_HF130_AEPn_1_06c / Plasmid: pJExpress / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: D0E8I5
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ODV / [(1R)-2-amino-1-hydroxyethyl]phosphonic acid


Mass: 141.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H8NO4P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 % PEG 5000 MME, 0.1 M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 9, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 22754 / Num. obs: 22671 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.3 % / Rsym value: 0.111 / Net I/σ(I): 12
Reflection shellResolution: 2.1→2.2 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4MLM

4mlm


Resolution: 2.1→19.9 Å / SU ML: 0.26 / σ(F): 2 / Phase error: 24.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2537 1133 5 %Random
Rwork0.1957 ---
obs0.1986 22669 99.79 %-
all-22669 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2801 0 20 138 2959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122893
X-RAY DIFFRACTIONf_angle_d0.9933927
X-RAY DIFFRACTIONf_dihedral_angle_d14.1431027
X-RAY DIFFRACTIONf_chiral_restr0.065416
X-RAY DIFFRACTIONf_plane_restr0.004501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19550.30361380.21872630X-RAY DIFFRACTION100
2.1955-2.31110.24711390.21192641X-RAY DIFFRACTION100
2.3111-2.45570.31291410.20282663X-RAY DIFFRACTION100
2.4557-2.64490.28151400.20412659X-RAY DIFFRACTION100
2.6449-2.91030.29931410.2072678X-RAY DIFFRACTION100
2.9103-3.32970.26671420.20612711X-RAY DIFFRACTION100
3.3297-4.18860.25871430.17552722X-RAY DIFFRACTION100
4.1886-19.90130.20481490.19232832X-RAY DIFFRACTION100

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