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- PDB-3l8e: Crystal Structure of apo form of D,D-heptose 1.7-bisphosphate pho... -

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Basic information

Entry
Database: PDB / ID: 3l8e
TitleCrystal Structure of apo form of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli
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,D-heptose 1,7-bisphosphate phosphatase activity / D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase / 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
ACETIC ACID / 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: 1.64 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 1.3Feb 21, 2024Group: 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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_seq_id / _struct_conn.ptnr2_label_asym_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
B: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0386
Polymers41,7872
Non-polymers2514
Water6,810378
1
A: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0193
Polymers20,8941
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D,D-heptose 1,7-bisphosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0193
Polymers20,8941
Non-polymers1252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.766, 63.967, 103.196
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 20893.727 Da / Num. of mol.: 2
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
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: X12B / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 17, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 76862 / % possible obs: 99.4 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
1.64-1.76.10.49198.4
1.7-1.776.10.36298.7
1.77-1.856.20.28899.2
1.85-1.946.20.19899.3
1.94-2.076.30.13899.6
2.07-2.236.30.10899.6
2.23-2.456.50.08999.8
2.45-2.86.70.065100
2.8-3.536.80.046100
3.53-506.40.04199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→25.105 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.19 / σ(F): 1 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 7540 9.81 %
Rwork0.1696 --
obs0.1737 76862 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.485 Å2 / ksol: 0.419 e/Å3
Displacement parametersBiso mean: 16.872 Å2
Baniso -1Baniso -2Baniso -3
1--0.586 Å2-0 Å20 Å2
2---3.086 Å2-0 Å2
3---3.672 Å2
Refinement stepCycle: LAST / Resolution: 1.64→25.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 0 10 378 3276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062958
X-RAY DIFFRACTIONf_angle_d1.0654013
X-RAY DIFFRACTIONf_dihedral_angle_d18.0311073
X-RAY DIFFRACTIONf_chiral_restr0.069442
X-RAY DIFFRACTIONf_plane_restr0.005529
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65870.25552080.2192132X-RAY DIFFRACTION88
1.6587-1.67820.24812240.22082081X-RAY DIFFRACTION84
1.6782-1.69860.25141980.21432158X-RAY DIFFRACTION88
1.6986-1.72010.25422180.20232127X-RAY DIFFRACTION86
1.7201-1.74280.23292390.19132161X-RAY DIFFRACTION90
1.7428-1.76660.24342500.18622171X-RAY DIFFRACTION90
1.7666-1.79190.19782110.18612308X-RAY DIFFRACTION91
1.7919-1.81860.20732010.18312206X-RAY DIFFRACTION90
1.8186-1.8470.2242490.17072303X-RAY DIFFRACTION93
1.847-1.87730.2182700.17572192X-RAY DIFFRACTION92
1.8773-1.90960.25632570.16592298X-RAY DIFFRACTION94
1.9096-1.94430.21572820.17272250X-RAY DIFFRACTION94
1.9443-1.98170.23292640.17612312X-RAY DIFFRACTION96
1.9817-2.02220.23162360.15742383X-RAY DIFFRACTION97
2.0222-2.06610.1852850.15632355X-RAY DIFFRACTION96
2.0661-2.11410.20662840.16322258X-RAY DIFFRACTION96
2.1141-2.1670.2052520.15582387X-RAY DIFFRACTION96
2.167-2.22550.18732900.15442313X-RAY DIFFRACTION97
2.2255-2.2910.19822360.15942384X-RAY DIFFRACTION97
2.291-2.36490.2092920.16182352X-RAY DIFFRACTION97
2.3649-2.44930.20182500.16862380X-RAY DIFFRACTION98
2.4493-2.54730.22252840.17282359X-RAY DIFFRACTION98
2.5473-2.66310.24232770.17462433X-RAY DIFFRACTION99
2.6631-2.80340.23532320.16982439X-RAY DIFFRACTION99
2.8034-2.97870.20132400.1632430X-RAY DIFFRACTION99
2.9787-3.20830.19792300.16442497X-RAY DIFFRACTION99
3.2083-3.53040.17382610.14692403X-RAY DIFFRACTION100
3.5304-4.03940.16683220.14922376X-RAY DIFFRACTION99
4.0394-5.08230.20442180.1532482X-RAY DIFFRACTION100
5.0823-25.10830.22622800.19312392X-RAY DIFFRACTION99

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