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- PDB-4pnh: Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase fro... -

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Basic information

Entry
Database: PDB / ID: 4pnh
TitleCrystal structure of D,D-heptose 1,7-bisphosphate phosphatase from Burkholderia Thailandensis
ComponentsD,D-heptose 1,7-bisphosphate phosphatase
KeywordsHYDROLASE / GMHB / ALPHA/BETA / PHOSPHATASE / D / D-HEPTOSE 1 / 7-BISPHOSPHATE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / 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,D-heptose 1,7-bisphosphate phosphatase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsKim, M.S. / Shin, D.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
national research foundation of Korea2013R1A1A1A05008769, 2010-0003907 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of D,D-heptose 1,7-bisphosphate phosphatase from Burkholderia Thailandensis
Authors: Kim, M.S. / Shin, D.H.
History
DepositionMay 23, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionJun 24, 2015ID: 4JYR
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Derived calculations
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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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
C: D,D-heptose 1,7-bisphosphate phosphatase
D: D,D-heptose 1,7-bisphosphate phosphatase
E: D,D-heptose 1,7-bisphosphate phosphatase
F: D,D-heptose 1,7-bisphosphate phosphatase
G: D,D-heptose 1,7-bisphosphate phosphatase
H: D,D-heptose 1,7-bisphosphate phosphatase
I: D,D-heptose 1,7-bisphosphate phosphatase
J: D,D-heptose 1,7-bisphosphate phosphatase
K: D,D-heptose 1,7-bisphosphate phosphatase
L: D,D-heptose 1,7-bisphosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)256,42212
Polymers256,42212
Non-polymers00
Water1629
1
A: D,D-heptose 1,7-bisphosphate phosphatase
H: D,D-heptose 1,7-bisphosphate phosphatase
I: D,D-heptose 1,7-bisphosphate phosphatase
J: D,D-heptose 1,7-bisphosphate phosphatase
K: D,D-heptose 1,7-bisphosphate phosphatase
L: D,D-heptose 1,7-bisphosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)128,2116
Polymers128,2116
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D,D-heptose 1,7-bisphosphate phosphatase
C: D,D-heptose 1,7-bisphosphate phosphatase
D: D,D-heptose 1,7-bisphosphate phosphatase
E: D,D-heptose 1,7-bisphosphate phosphatase
F: D,D-heptose 1,7-bisphosphate phosphatase
G: D,D-heptose 1,7-bisphosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)128,2116
Polymers128,2116
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)245.904, 245.904, 41.398
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
D,D-heptose 1,7-bisphosphate phosphatase


Mass: 21368.496 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I0583 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2T109, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.8 / Details: 1.3M AMMONIUM SULFATE, 0.1M SODIUM ACETATE PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2009
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→48.86 Å / Num. obs: 70758 / % possible obs: 87.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.8
Reflection shellResolution: 2.66→2.71 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.1 / % possible all: 86.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1420) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→35.01 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2529 3945 5.58 %
Rwork0.2142 --
obs0.2162 70718 87.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→35.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13968 0 0 9 13977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01214189
X-RAY DIFFRACTIONf_angle_d1.17319116
X-RAY DIFFRACTIONf_dihedral_angle_d12.1025160
X-RAY DIFFRACTIONf_chiral_restr0.0462208
X-RAY DIFFRACTIONf_plane_restr0.0052472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6597-2.70540.33631850.30543268X-RAY DIFFRACTION81
2.7054-2.75450.32961780.29723466X-RAY DIFFRACTION84
2.7545-2.80740.32311770.28583331X-RAY DIFFRACTION85
2.8074-2.86460.33141620.28513521X-RAY DIFFRACTION88
2.8646-2.92670.29811730.2713558X-RAY DIFFRACTION88
2.9267-2.99460.32431760.26643563X-RAY DIFFRACTION87
2.9946-3.06920.30781920.25793463X-RAY DIFFRACTION88
3.0692-3.1520.31122110.25083665X-RAY DIFFRACTION90
3.152-3.24440.27141900.22333483X-RAY DIFFRACTION87
3.2444-3.34870.2191900.21543485X-RAY DIFFRACTION88
3.3487-3.46790.25562130.21133580X-RAY DIFFRACTION87
3.4679-3.60610.25511380.21692755X-RAY DIFFRACTION70
3.6061-3.76930.23991600.19473162X-RAY DIFFRACTION77
3.7693-3.96680.2121560.18393334X-RAY DIFFRACTION84
3.9668-4.21350.22791910.18513419X-RAY DIFFRACTION85
4.2135-4.53580.20251770.1623455X-RAY DIFFRACTION86
4.5358-4.98670.19761700.15673289X-RAY DIFFRACTION83
4.9867-5.69580.25241780.2023275X-RAY DIFFRACTION82
5.6958-7.12940.26531690.23183183X-RAY DIFFRACTION79
7.1294-21.03910.25941530.22892860X-RAY DIFFRACTION71

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