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- PDB-2oda: Crystal Structure of PSPTO_2114 -

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Basic information

Entry
Database: PDB / ID: 2oda
TitleCrystal Structure of PSPTO_2114
ComponentsHypothetical protein PSPTO_2114
KeywordsPROTEIN BINDING / Haloacid dehalogenase / phosphonoacetaldehyde hydrolase
Function / homologyHAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / HAD family phosphatase
Function and homology information
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsPeisach, E. / Allen, K.N. / Dunaway-Mariano, D. / Wang, L. / Burroughs, A.M. / Aravind, L.
Citation
Journal: Proteins / Year: 2007
Title: The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function.
Authors: Peisach, E. / Wang, L. / Burroughs, A.M. / Aravind, L. / Dunaway-Mariano, D. / Allen, K.N.
#1: Journal: Biochemistry / Year: 2000
Title: The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily
Authors: Morais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionDec 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: 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_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein PSPTO_2114
B: Hypothetical protein PSPTO_2114
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6695
Polymers42,1692
Non-polymers5013
Water9,638535
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.612, 74.427, 106.354
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein PSPTO_2114


Mass: 21084.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Species: Pseudomonas syringae group genomosp. 3 / Gene: PSPTO_2114 / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q884H9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.9 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 15-20% PEG 3350, 150-200mM Sodium formate, 100mM Hepes pH 7.3, 5mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97980, 0.97786, 0.95000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005
RadiationMonochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.977861
30.951
ReflectionResolution: 1.9→60 Å / Num. all: 30874 / Num. obs: 30874 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 13.45 Å2 / Rsym value: 0.065 / Net I/σ(I): 41
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 2580 / Rsym value: 0.183 / % possible all: 83.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.1 Å / D res low: 20 Å / FOM : 0.77 / Reflection: 22986
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97985.49-5.78
13 wavelength20.97792.94-8.49
13 wavelength30.954.06-2.5
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se18.610.6690.3080.2530.897
2Se16.3620.9450.6920.2070.789
3Se19.6140.770.3070.2270.759
4Se11.2860.4080.160.1890.766
5Se17.9420.4480.2620.1170.801
6Se18.7140.0030.7930.1410.753
7Se27.6040.2880.8470.2280.695
8Se31.5680.720.3450.1990.674
Phasing MAD shell
Resolution (Å)FOM Reflection
7.31-200.921226
4.7-7.310.921960
3.7-4.70.92451
3.15-3.70.892850
2.79-3.150.823215
2.52-2.790.753500
2.33-2.520.663778
2.17-2.330.564006
Phasing dmFOM : 0.84 / FOM acentric: 0.85 / FOM centric: 0.79 / Reflection: 22988 / Reflection acentric: 20209 / Reflection centric: 2779
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.9870.960.980.931061746315
3.8-60.960.980.9131602606554
3-3.80.940.950.8738883379509
2.6-30.890.90.7938983467431
2.3-2.60.790.80.6967976169628
2.1-2.30.680.690.5741843842342

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Processing

Software
NameVersionClassificationNB
SOLVE2.11phasing
RESOLVE2.11phasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.958 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.219 3024 9.9 %RANDOM
Rwork0.167 ---
all0.172 ---
obs-30590 97.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2879 0 31 535 3445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222980
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.994073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.625385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.33825116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80215455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3941516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022262
X-RAY DIFFRACTIONr_nbd_refined0.1960.21495
X-RAY DIFFRACTIONr_nbtor_refined0.2950.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2446
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.256
X-RAY DIFFRACTIONr_mcbond_it0.931.51991
X-RAY DIFFRACTIONr_mcangle_it1.18823084
X-RAY DIFFRACTIONr_scbond_it2.03431142
X-RAY DIFFRACTIONr_scangle_it2.9994.5989
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 162 -
Rwork0.164 1701 -
obs-1863 81.07 %

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