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- PDB-2hsz: Crystal structure of a predicted phosphoglycolate phosphatase (hs... -

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Basic information

Entry
Database: PDB / ID: 2hsz
TitleCrystal structure of a predicted phosphoglycolate phosphatase (hs_0176) from haemophilus somnus 129pt at 1.90 A resolution
Componentsnovel predicted phosphatase
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / glycolate biosynthetic process / carbohydrate metabolic process / DNA repair / metal ion binding / cytosol
Similarity search - Function
Phosphoglycolate phosphatase, prokaryotic / Hypothetical cof family signature 1. / : / 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 superfamily ...Phosphoglycolate phosphatase, prokaryotic / Hypothetical cof family signature 1. / : / 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 superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Unknown ligand / Phosphoglycolate phosphatase
Similarity search - Component
Biological speciesHaemophilus somnus 129PT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of novel predicted phosphatase from Haemophilus somnus 129PT at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 24, 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 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300REMARK 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...REMARK 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE A suitable database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: novel predicted phosphatase
B: novel predicted phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2948
Polymers55,1052
Non-polymers1896
Water6,017334
1
A: novel predicted phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6474
Polymers27,5531
Non-polymers943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: novel predicted phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6474
Polymers27,5531
Non-polymers943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.617, 118.436, 66.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 4 / Auth seq-ID: 1 - 224 / Label seq-ID: 20 - 243

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE

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Components

#1: Protein novel predicted phosphatase


Mass: 27552.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus somnus 129PT (bacteria) / Species: Histophilus somni / Production host: Escherichia coli (E. coli) / References: UniProt: Q0I1W8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.93 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 277 K / pH: 7.9
Details: 0.2M NaAcetate, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97925,1.28281,0.97914
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 8, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979251
31.282811
40.979141
ReflectionResolution: 1.897→29.988 Å / Num. obs: 51412 / % possible obs: 100 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.953.70.65311379037440.653100
1.95-23.70.4951.41348336530.495100
2-2.063.70.3871.91311435520.387100
2.06-2.123.70.312.11271734470.31100
2.12-2.193.70.2452.91256233910.245100
2.19-2.273.70.23.61188632200.2100
2.27-2.363.70.1734.31163231440.173100
2.36-2.453.70.1395.21122330270.139100
2.45-2.563.70.1176.31084029300.117100
2.56-2.693.70.0977.61020527680.097100
2.69-2.833.70.0799984026630.079100
2.83-34.90.0976.51235925140.097100
3-3.217.80.16.61839023630.1100
3.21-3.477.80.0798.11725022250.079100
3.47-3.87.70.0639.71574920360.063100
3.8-4.257.70.05312.11444118830.053100
4.25-4.917.60.05311.51258116520.053100
4.91-6.017.50.069.11067914240.06100
6.01-8.57.30.05510.2828111270.05599.9
8.5-29.996.80.059.744066490.0597.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.988 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.066 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.112
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 ...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). THERE ARE UNKNOWN DENSITY NEAR ACTIVE SITE IN A AND B CHAINS. THEY ARE NAMED AS UNL. (4). THERE ARE UNKNOWN DENSITY NEAR PHE 75 IN A AND B MOLECULES, TYR 77 AND PHE 138 IN A MOLECULE, PRO 152 AND TYR 200 IN B MOLECULE. THEY ARE ALL IN THE SOLVENT REGION AND LEFT UNMODELED. (5). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2613 5.1 %RANDOM
Rwork0.169 ---
obs0.171 51362 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.69 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.7 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 30 334 3881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223660
X-RAY DIFFRACTIONr_bond_other_d0.0010.022406
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9594988
X-RAY DIFFRACTIONr_angle_other_deg0.94835916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7755462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.88825.422166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90715586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.593156
X-RAY DIFFRACTIONr_chiral_restr0.0930.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02730
X-RAY DIFFRACTIONr_nbd_refined0.2460.2773
X-RAY DIFFRACTIONr_nbd_other0.1820.22355
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21818
X-RAY DIFFRACTIONr_nbtor_other0.0860.21734
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.211
X-RAY DIFFRACTIONr_mcbond_it2.0932352
X-RAY DIFFRACTIONr_mcbond_other0.6513916
X-RAY DIFFRACTIONr_mcangle_it2.83153656
X-RAY DIFFRACTIONr_scbond_it4.6181542
X-RAY DIFFRACTIONr_scangle_it6.555111326
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2896 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.180.5
MEDIUM THERMAL0.932
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 179 -
Rwork0.225 3476 -
obs-3655 97.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7797-0.04720.11781.11290.22911.2728-0.1011-0.06110.05820.06060.01490.0516-0.19240.01950.0862-0.03540.0292-0.0259-0.0682-0.0049-0.0684-7.746777.661617.4957
20.26880.42120.09092.05020.52640.7795-0.03810.00180.0176-0.1479-0.02640.0897-0.0298-0.06040.0645-0.073-0.0292-0.0095-0.0386-0.0028-0.0531-11.568542.8474-11.8062
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 224 / Label seq-ID: 19 - 243

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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