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- PDB-3l8f: Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase fro... -

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Basic information

Entry
Database: PDB / ID: 3l8f
TitleCrystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli complexed with magnesium and phosphate
ComponentsD,D-heptose 1,7-bisphosphate phosphatase
KeywordsHYDROLASE / HAD superfamily / GMHB / D-glycero-D-manno-heptose-1 / 7-bisphosphate phosphatase / Carbohydrate metabolism / Cytoplasm / Lipopolysaccharide biosynthesis
Function / homology
Function and homology information


D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase activity / ADP-L-glycero-beta-D-manno-heptose biosynthetic process / lipopolysaccharide core region biosynthetic process / magnesium ion binding / zinc ion binding / cytosol
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
PHOSPHATE ION / D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsNguyen, H. / Peisach, E. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2010
Title: Structural Determinants of Substrate Recognition in the HAD Superfamily Member d-glycero-d-manno-Heptose-1,7-bisphosphate Phosphatase (GmhB) .
Authors: Nguyen, H.H. / Wang, L. / Huang, H. / Peisach, E. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionDec 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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_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.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.pdbx_leaving_atom_flag / _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_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_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: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4544
Polymers21,2691
Non-polymers1853
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.476, 50.002, 51.884
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

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Components

#1: Protein D,D-heptose 1,7-bisphosphate phosphatase / D-glycero-D-manno-heptose 1 / 7-bisphosphate phosphatase


Mass: 21268.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0200, gmhB, JW0196, yaeD / Plasmid: pET3 / Production host: Escherichia coli (E. coli) / Strain (production host): B-834
References: UniProt: P63228, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 1.97 Å3/Da / Density % sol: 37.44 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 0.1M Tris, 5mM MgCl2, 25% PEG 3350, pH 7.5, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 29102 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.048 / Χ2: 1.004 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.79-1.856.70.50816051.00299.9
1.85-1.936.70.34816001.002100
1.93-2.026.70.25316221.001100
2.02-2.126.70.1815901.00499.8
2.12-2.266.60.12416371.00699.7
2.26-2.436.70.09216090.99799.9
2.43-2.676.90.06916461.01199.9
2.67-3.066.80.04816381.00699.3
3.06-3.866.60.03316580.99698.9
3.86-506.50.02817531.01198.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.235 2844 9.3 %
Rwork0.191 --
obs-29102 95.3 %
Solvent computationBsol: 62.345 Å2
Displacement parametersBiso max: 79.24 Å2 / Biso mean: 32.033 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1-6.484 Å20 Å20 Å2
2---2.217 Å20 Å2
3----4.267 Å2
Refinement stepCycle: LAST / Resolution: 1.79→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 7 110 1549
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.3461.5
X-RAY DIFFRACTIONc_scbond_it3.7912
X-RAY DIFFRACTIONc_mcangle_it3.3792
X-RAY DIFFRACTIONc_scangle_it5.1382.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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