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- PDB-1ilv: Crystal Structure Analysis of the TM107 -

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Basic information

Entry
Database: PDB / ID: 1ilv
TitleCrystal Structure Analysis of the TM107
ComponentsSTATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / new fold / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


3'-nucleotidase activity / exopolyphosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
Stationary-phase Survival Protein Sure Homolog; Chain: A, / Survival protein SurE-like phosphatase/nucleotidase / Survival protein SurE / Survival protein SurE-like phosphatase/nucleotidase / SurE-like phosphatase/nucleotidase superfamily / Survival protein SurE / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-nucleotidase SurE
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsZhang, R. / Joachimiak, A. / Edwards, A. / Savchenko, A. / Beasley, S. / Evdokimova, E. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Structure / Year: 2001
Title: Structure of Thermotoga maritima stationary phase survival protein SurE: a novel acid phosphatase.
Authors: Zhang, R.G. / Skarina, T. / Katz, J.E. / Beasley, S. / Khachatryan, A. / Vyas, S. / Arrowsmith, C.H. / Clarke, S. / Edwards, A. / Joachimiak, A. / Savchenko, A.
History
DepositionMay 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Apr 3, 2024Group: 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG
B: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG


Theoretical massNumber of molelcules
Total (without water)57,2462
Polymers57,2462
Non-polymers00
Water4,540252
1
A: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG

A: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG


Theoretical massNumber of molelcules
Total (without water)57,2462
Polymers57,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area6760 Å2
ΔGint-51 kcal/mol
Surface area20290 Å2
MethodPISA, PQS
2
B: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG

B: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG


Theoretical massNumber of molelcules
Total (without water)57,2462
Polymers57,2462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6780 Å2
ΔGint-51 kcal/mol
Surface area20090 Å2
MethodPISA, PQS
3
A: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG

A: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG

B: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG

B: STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG


Theoretical massNumber of molelcules
Total (without water)114,4924
Polymers114,4924
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
crystal symmetry operation2_655-y+1,x-y,z+1/31
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area16080 Å2
ΔGint-121 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.522, 115.522, 78.666
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein STATIONARY-PHASE SURVIVAL PROTEIN SURE HOMOLOG / SurE protein / TM107


Mass: 28622.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P96112
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulphate, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
31.75 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793,0.9791,0.9639
DetectorType: SBC-1 / Detector: CCD / Date: Mar 23, 2001 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97911
30.96391
ReflectionResolution: 2→50 Å / Num. all: 41136 / Num. obs: 41136 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4052 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 79278 / % possible obs: 100 % / Num. measured all: 328134

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: wARP autotraced model

Resolution: 2→46.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 295098.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: used mlhl refinement target in CNS package
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3681 4.9 %RANDOM
Rwork0.244 ---
all-79278 --
obs-74997 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.62 Å2 / ksol: 0.368 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20.25 Å20 Å2
2---1.97 Å20 Å2
3---3.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→46.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3933 0 0 252 4185
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 504 4.5 %
Rwork0.33 10666 -
obs--84.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.9 % / Rfactor obs: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / % reflection Rfree: 4.5 % / Rfactor Rwork: 0.33

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