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- PDB-2o2x: Crystal structure of a putative had-like phosphatase (mll2559) fr... -

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Basic information

Entry
Database: PDB / ID: 2o2x
TitleCrystal structure of a putative had-like phosphatase (mll2559) from mesorhizobium loti at 1.50 A resolution
Componentshypothetical protein
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / phosphatase activity / carbohydrate metabolic process / metal ion binding / cytoplasm
Similarity search - Function
D,D-heptose 1,7-bisphosphate phosphatase / Histidinol-phosphate phosphatase / HAD-superfamily hydrolase,subfamily IIIA / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_103874.1) from Mesorhizobium loti at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7473
Polymers23,5631
Non-polymers1842
Water5,909328
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.480, 66.270, 41.020
Angle α, β, γ (deg.)90.000, 108.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein


Mass: 23563.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: NP_103874.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98I56
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 1.99 Å3/Da / Density % sol: 38.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.64
Details: 28.5% polyethylene glycol 6000, 0.1M HEPES pH 6.64, 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: 0.91837, 0.97978
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 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
10.918371
20.979781
ReflectionResolution: 1.5→28.262 Å / Num. obs: 29534 / % possible obs: 94.8 % / Redundancy: 3.71 % / Biso Wilson estimate: 12.94 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.5-1.550.2712.888560452788.8
1.55-1.620.2083.911711585688.6
1.62-1.690.1674.89909497090.7
1.69-1.780.127610749538791.3
1.78-1.890.0997.710661534392.2
1.89-2.040.06910.511124559493.8
2.04-2.240.05113.510756540495
2.24-2.560.03816.511028554695.6
2.560.03419.911221569096.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→28.262 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.152 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.067
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 1499 5.1 %RANDOM
Rwork0.138 ---
obs0.139 29513 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.085 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.75 Å2
2---0.22 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 12 328 1906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221651
X-RAY DIFFRACTIONr_bond_other_d0.0010.021583
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9872256
X-RAY DIFFRACTIONr_angle_other_deg0.82633662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6455219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74123.04369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8415257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7131516
X-RAY DIFFRACTIONr_chiral_restr0.0840.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021863
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_nbd_refined0.2070.2316
X-RAY DIFFRACTIONr_nbd_other0.1870.21638
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2796
X-RAY DIFFRACTIONr_nbtor_other0.0810.2989
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.236
X-RAY DIFFRACTIONr_mcbond_it1.7231128
X-RAY DIFFRACTIONr_mcbond_other0.4053430
X-RAY DIFFRACTIONr_mcangle_it2.33751702
X-RAY DIFFRACTIONr_scbond_it3.6218637
X-RAY DIFFRACTIONr_scangle_it5.5911548
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 103 -
Rwork0.188 2028 -
obs-2131 97.48 %

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