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- PDB-4b6j: Crystal structure of phosphoserine phosphatase from T. onnurineus -

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Basic information

Entry
Database: PDB / ID: 4b6j
TitleCrystal structure of phosphoserine phosphatase from T. onnurineus
ComponentsPHOSPHOSERINE PHOSPHATASE
KeywordsHYDROLASE / L-SERINE / HALOACID DEHALOGENASE SUPERFAMILY
Function / homology
Function and homology information


phosphoserine phosphatase
Similarity search - Function
Phosphoserine phosphatase; domain 2 / haloacid dehalogenase-like hydrolase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Phosphoserine phosphatase; domain 2 / haloacid dehalogenase-like hydrolase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
phosphoserine phosphatase
Similarity search - Component
Biological speciesTHERMOCOCCUS ONNURINEUS NA1 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsJung, T.-Y. / Kim, Y.-S. / Song, H.-N. / Woo, E.
CitationJournal: Proteins / Year: 2013
Title: Identification of a Novel Ligand Binding Site in Phosphoserine Phosphatase from the Hyperthermophilic Archaeon Thermococcus Onnurineus.
Authors: Jung, T.-Y. / S-Kim, Y. / Oh, B.H. / Woo, E.
History
DepositionAug 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)92,0754
Polymers92,0754
Non-polymers00
Water0
1
A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE

A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)184,1498
Polymers184,1498
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area23030 Å2
ΔGint-91 kcal/mol
Surface area61310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.281, 89.281, 228.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND (RESSEQ 10:190))
211(CHAIN B AND (RESSEQ 10:190))

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Components

#1: Protein
PHOSPHOSERINE PHOSPHATASE /


Mass: 23018.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS ONNURINEUS NA1 (archaea) / Production host: ESCHERICHIA COLI MC1061 (bacteria) / Variant (production host): ARAD139, GALE15, GALK16 / References: UniProt: B6YX36, phosphoserine phosphatase

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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: 2.61 Å3/Da / Density % sol: 52.9 % / Description: NONE
Crystal growpH: 6.5
Details: 30% PENTAERYTHRITOL ETHOXYLATE, 50 MM BIS-TRIS PH 6.5, 50 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV / Detector: IMAGE PLATE / Date: Sep 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.34→44.64 Å / Num. obs: 14085 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 66.18 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 9.1
Reflection shellResolution: 3.34→3.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AP9

4ap9


Resolution: 3.34→44.641 Å / SU ML: 0.36 / σ(F): 1.34 / Phase error: 23.9 / Stereochemistry target values: MLHL
Details: -6 GLY TO 0 PHE WERE PURIFICATION TAG PRO194 REGION WAS DISORDERED
RfactorNum. reflection% reflection
Rfree0.2625 707 5 %
Rwork0.2144 --
obs0.2168 14085 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.63 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 3.34→44.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6412 0 0 0 6412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056508
X-RAY DIFFRACTIONf_angle_d0.9098688
X-RAY DIFFRACTIONf_dihedral_angle_d14.8762520
X-RAY DIFFRACTIONf_chiral_restr0.057936
X-RAY DIFFRACTIONf_plane_restr0.0041128
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11AX-RAY DIFFRACTIONPOSITIONAL
12BX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3402-3.5980.34411570.26042588X-RAY DIFFRACTION100
3.598-3.95990.27661420.2162624X-RAY DIFFRACTION100
3.9599-4.53240.24831350.18722649X-RAY DIFFRACTION100
4.5324-5.70850.22751460.19642676X-RAY DIFFRACTION100
5.7085-44.64450.25461270.22892841X-RAY DIFFRACTION99

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