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- PDB-4ap9: Crystal structure of phosphoserine phosphatase from T. onnurineus... -

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Basic information

Entry
Database: PDB / ID: 4ap9
TitleCrystal structure of phosphoserine phosphatase from T. onnurineus in complex with NDSB-201
ComponentsPHOSPHOSERINE PHOSPHATASE
KeywordsHYDROLASE / HALOACID DEHALOGENASE SUPERFAMILY / NDSB
Function / homology
Function and homology information


phosphoserine phosphatase / L-serine biosynthetic process / hydrolase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Phosphoserine phosphatase; domain 2 / haloacid dehalogenase-like hydrolase / : / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle ...Phosphoserine phosphatase; domain 2 / haloacid dehalogenase-like hydrolase / : / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / phosphoserine phosphatase
Similarity search - Component
Biological speciesTHERMOCOCCUS ONNURINEUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.783 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
DepositionMar 31, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_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: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,59510
Polymers93,3884
Non-polymers1,2076
Water15,601866
1
A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
hetero molecules

A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
hetero molecules

A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
hetero molecules

A: PHOSPHOSERINE PHOSPHATASE
B: PHOSPHOSERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,19020
Polymers186,7758
Non-polymers2,41512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation2_555-x,-y,z1
Buried area27330 Å2
ΔGint-53.9 kcal/mol
Surface area62930 Å2
MethodPISA
2
C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE
hetero molecules

C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE
hetero molecules

C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE
hetero molecules

C: PHOSPHOSERINE PHOSPHATASE
D: PHOSPHOSERINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,19020
Polymers186,7758
Non-polymers2,41512
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
crystal symmetry operation4_455y-1,-x,z1
crystal symmetry operation3_565-y,x+1,z1
Buried area27600 Å2
ΔGint-47 kcal/mol
Surface area62660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.131, 128.131, 63.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

#1: Protein
PHOSPHOSERINE PHOSPHATASE


Mass: 23346.908 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOCOCCUS ONNURINEUS (archaea) / Description: ARAD139, GALE15, GALK16 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: B6YX36, phosphoserine phosphatase
#2: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6.5 / Details: 1.45M SODIUM CITRATE, 0.2M NDSB-201, pH 6.5

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.979
DetectorDate: Feb 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→28.65 Å / Num. obs: 91927 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 17.33 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.4
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVERESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.783→28.651 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 21.69 / Stereochemistry target values: ML
Details: RESIDUE -6 TO 0 ARE DERIVED FROM PURIFICATION TAG IN EACH MONOMER
RfactorNum. reflection% reflection
Rfree0.2206 4592 5 %
Rwork0.1951 --
obs0.1964 91927 94.16 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.361 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso mean: 19.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.0086 Å20 Å20 Å2
2---1.0086 Å20 Å2
3---2.0173 Å2
Refinement stepCycle: LAST / Resolution: 1.783→28.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 78 866 7384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076614
X-RAY DIFFRACTIONf_angle_d1.0598826
X-RAY DIFFRACTIONf_dihedral_angle_d14.7352582
X-RAY DIFFRACTIONf_chiral_restr0.07936
X-RAY DIFFRACTIONf_plane_restr0.0041142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7834-1.84710.26924400.22438018X-RAY DIFFRACTION87
1.8471-1.9210.25814000.22348430X-RAY DIFFRACTION91
1.921-2.00850.24144720.21558577X-RAY DIFFRACTION93
2.0085-2.11430.25224830.20658628X-RAY DIFFRACTION94
2.1143-2.24670.24634590.19598690X-RAY DIFFRACTION94
2.2467-2.42010.23694240.19498773X-RAY DIFFRACTION94
2.4201-2.66350.26234510.21488836X-RAY DIFFRACTION96
2.6635-3.04850.22834710.21698955X-RAY DIFFRACTION96
3.0485-3.83940.19154520.17629082X-RAY DIFFRACTION97
3.8394-28.65460.18365400.17419346X-RAY DIFFRACTION99

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