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- PDB-6d3w: Chromosomal trehalose-6-phosphate phosphatase from P. aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6d3w
TitleChromosomal trehalose-6-phosphate phosphatase from P. aeruginosa
ComponentsTrehalose phosphatase
KeywordsLYASE / HAD SUPERFAMILY/ROSSMANN FOLD / TREHALOSE-6-PHOSPHATE / PHOSPHOHYDROLASE / HYDROLASE
Function / homologyTrehalose phosphatase-like / HAD superfamily / HAD-like superfamily / metal ion binding / ACETIC ACID / Trehalose phosphatase
Function and homology information
Biological speciesPseudomonas sp. HMSC75E02 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHofmann, A. / Cross, M. / Park, S.-Y.
CitationJournal: FASEB J. / Year: 2018
Title: Trehalose 6-phosphate phosphatases of Pseudomonas aeruginosa.
Authors: Cross, M. / Biberacher, S. / Park, S.Y. / Rajan, S. / Korhonen, P. / Gasser, R.B. / Kim, J.S. / Coster, M.J. / Hofmann, A.
History
DepositionApr 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_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_comp_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trehalose phosphatase
B: Trehalose phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,82912
Polymers56,2562
Non-polymers57310
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-33 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.030, 66.847, 75.263
Angle α, β, γ (deg.)90.00, 119.48, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(chain A and (resid -1 through 110 or resid 112 through 249))
211(chain B and (resid -1 through 110 or resid 112 through 249))

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Components

#1: Protein Trehalose phosphatase


Mass: 28128.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. HMSC75E02 (bacteria) / Gene: HMPREF3289_15950 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S1GKD7
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2 M MGCL2, 20% PEG 6000, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97957 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97957 Å / Relative weight: 1
ReflectionResolution: 1.9→24.25 Å / Num. obs: 50404 / % possible obs: 99.7 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.044 / Rrim(I) all: 0.096 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7303 / CC1/2: 0.801 / Rpim(I) all: 0.323 / Rrim(I) all: 0.698 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cj0
Resolution: 1.9→24.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.2193 2507 4.98 %
Rwork0.1756 --
obs0.1777 50312 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3894 0 34 227 4155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074038
X-RAY DIFFRACTIONf_angle_d0.8375460
X-RAY DIFFRACTIONf_dihedral_angle_d15.0132380
X-RAY DIFFRACTIONf_chiral_restr0.052592
X-RAY DIFFRACTIONf_plane_restr0.005710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1933X-RAY DIFFRACTIONPOSITIONAL
12B1933X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93650.35981470.2762606X-RAY DIFFRACTION99
1.9365-1.97610.30051450.2182616X-RAY DIFFRACTION99
1.9761-2.0190.22561340.19742663X-RAY DIFFRACTION100
2.019-2.06590.27761510.19232595X-RAY DIFFRACTION100
2.0659-2.11760.21811160.19712662X-RAY DIFFRACTION100
2.1176-2.17480.2871250.18372668X-RAY DIFFRACTION100
2.1748-2.23880.21471360.17532682X-RAY DIFFRACTION100
2.2388-2.3110.23761360.18082628X-RAY DIFFRACTION100
2.311-2.39350.3122720.19142756X-RAY DIFFRACTION100
2.3935-2.48920.24051360.19192634X-RAY DIFFRACTION100
2.4892-2.60240.23881780.18462623X-RAY DIFFRACTION100
2.6024-2.73940.25631370.19782684X-RAY DIFFRACTION100
2.7394-2.91080.22041520.18832632X-RAY DIFFRACTION100
2.9108-3.13510.21121500.19542682X-RAY DIFFRACTION100
3.1351-3.44980.22631660.17842643X-RAY DIFFRACTION100
3.4498-3.94710.20541600.16162660X-RAY DIFFRACTION100
3.9471-4.9660.15891250.12642725X-RAY DIFFRACTION100
4.966-24.25370.17861410.16452646X-RAY DIFFRACTION96
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.62550.1955-0.23840.64590.16820.61990.0904-0.00730.07860.0133-0.0751-0.0643-0.06780.0558-0.00070.1822-0.00260.00960.15940.0280.170467.9487-8.320124.5451
21.0032-0.95360.05771.8954-0.33231.1356-0.01230.5920.5435-0.0803-0.005-0.1699-0.18150.07680.12340.25730.02520.07210.5740.26790.417679.2424-3.94023.1963
31.0069-0.0240.11671.1484-0.58371.11650.04490.2381-0.0523-0.114-0.067-0.0790.03940.034-0.00220.18260.02930.01320.1930.01450.178566.4151-17.450614.5866
40.60750.13140.29040.6183-0.07910.65350.09310.0061-0.09250.0025-0.07320.06330.0623-0.0636-0.0010.1833-0.007-0.00740.1648-0.03140.173542.59-28.211824.217
51.231-0.9394-0.03981.88430.35641.1787-0.03730.5793-0.5818-0.05890.01220.18280.257-0.0060.08710.2963-0.0044-0.05910.5814-0.27620.451432.1671-33.96072.9859
61.0271-0.0025-0.13651.14360.54881.01650.04140.2690.0601-0.1507-0.06040.0705-0.0808-0.06070.00590.18880.0325-0.01090.2126-0.01170.177544.0972-19.449314.0028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:107)
2X-RAY DIFFRACTION2(chain A and resid 108:177)
3X-RAY DIFFRACTION3(chain A and resid 178:251)
4X-RAY DIFFRACTION4(chain B and resid -1:110)
5X-RAY DIFFRACTION5(chain B and resid 111:174)
6X-RAY DIFFRACTION6(chain B and resid 175:251)

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