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- PDB-2hdo: Crystal structure of putative phosphoglycolate phosphatase (np_78... -

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Basic information

Entry
Database: PDB / ID: 2hdo
TitleCrystal structure of putative phosphoglycolate phosphatase (np_784602.1) from Lactobacillus plantarum at 1.50 A resolution
ComponentsPhosphoglycolate phosphatase
KeywordsHYDROLASE / np_784602.1 / putative phosphoglycolate phosphatase / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphohydrolase / :
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative phosphoglycolate phosphatase (np_784602.1) from Lactobacillus plantarum at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycolate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0253
Polymers23,8351
Non-polymers1902
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.890, 86.890, 47.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Phosphoglycolate phosphatase /


Mass: 23835.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: np_784602.1, gph1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q88YA8, UniProt: F9UM81*PLUS, phosphoglycolate phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 0.4M KH2PO3, 1.6M NaH2PO3, 0.1M Phosphate Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979224, 0.978954, 0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9792241
20.9789541
30.918371
ReflectionResolution: 1.5→29.424 Å / Num. obs: 32658 / % possible obs: 96.5 % / Redundancy: 8.784 % / Biso Wilson estimate: 22.126 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 7.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.5-1.550.4262.3211737424688.8
1.55-1.620.3822.918629644989
1.62-1.690.3173.515873549090.6
1.69-1.780.4474.423105591891.5
1.78-1.890.4685.334402592893.2
1.89-2.040.3566.633794594991.3
2.04-2.240.2378.134138605796.4
2.24-2.560.1639.934882620597.6
2.560.11312.836393637298.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.424 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.408 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.081
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3.DUE TO SEVERAL STRONG ICE RINGS, 1316 REFLECTIONS WITH INTENSITIES >=15 * (EXPECTED MEAN INTENSITY) BETWEEN 1.516-1.533, 1.890-1.930, 2.025-2.080, 2.210-2.289 ANGSTROMS WERE OMITTED FROM THE FINAL REFINEMENT. 4.TWO PHOSPHATE IONS FROM CRYSTALLIZATION BUFFER WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 1564 5.1 %RANDOM
Rwork0.176 ---
obs0.178 30840 95.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.763 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.33 Å20 Å2
2---0.65 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.424 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 10 212 1796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221665
X-RAY DIFFRACTIONr_bond_other_d0.0010.021489
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9642278
X-RAY DIFFRACTIONr_angle_other_deg0.80833468
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755220
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02724.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.15715265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.608157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
X-RAY DIFFRACTIONr_nbd_refined0.2290.2377
X-RAY DIFFRACTIONr_nbd_other0.1730.21473
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2835
X-RAY DIFFRACTIONr_nbtor_other0.0860.2940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0880.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.120.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.212
X-RAY DIFFRACTIONr_mcbond_it1.98431093
X-RAY DIFFRACTIONr_mcbond_other0.4863420
X-RAY DIFFRACTIONr_mcangle_it2.76551727
X-RAY DIFFRACTIONr_scbond_it4.5788643
X-RAY DIFFRACTIONr_scangle_it6.50411546
LS refinement shellResolution: 1.504→1.543 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 84 -
Rwork0.295 1597 -
obs-1681 70.31 %
Refinement TLS params.Method: refined / Origin x: 24.3027 Å / Origin y: 21.9784 Å / Origin z: 22.2181 Å
111213212223313233
T-0.0187 Å20.0106 Å20.0093 Å2--0.0232 Å20.0104 Å2---0.0273 Å2
L0.6919 °2-0.1209 °20.1494 °2-0.7872 °20.5101 °2--0.7208 °2
S-0.0157 Å °0.0103 Å °0.0008 Å °0.0465 Å °0.0182 Å °0.0121 Å °0.0598 Å °0.0418 Å °-0.0025 Å °
Refinement TLS groupSelection: ALL

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