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- PDB-1zpv: ACT domain protein from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 1zpv
TitleACT domain protein from Streptococcus pneumoniae
ComponentsACT domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ACT domain / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Uncharacterised protein family UPF0237, ACT-type / : / ACT domain / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / UPF0237 protein SP_0238
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsOsipiuk, J. / Hatzos, C. / Abdullah, J. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of ACT domain protein from Streptococcus pneumoniae
Authors: Osipiuk, J. / Hatzos, C. / Abdullah, J. / Collart, F. / Joachimiak, A.
History
DepositionMay 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS NOT YET KNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACT domain protein
B: ACT domain protein
C: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4534
Polymers30,4143
Non-polymers391
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ACT domain protein
C: ACT domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3153
Polymers20,2762
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-18 kcal/mol
Surface area8550 Å2
MethodPISA, PQS
3
B: ACT domain protein

B: ACT domain protein


Theoretical massNumber of molelcules
Total (without water)20,2762
Polymers20,2762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2100 Å2
ΔGint-17 kcal/mol
Surface area8240 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)109.253, 62.024, 38.006
Angle α, β, γ (deg.)90.00, 95.08, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-157-

HOH

Detailsthe biological assembly is unknown

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Components

#1: Protein ACT domain protein


Mass: 10137.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP0238 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P67382
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.1 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate, 0.1 M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97929 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 9, 2005
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 19284 / Num. obs: 19284 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 30.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.21 / Num. unique all: 1020 / % possible all: 73.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.952 / SU B: 4.896 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ALL DATA WERE USED IN FINAL ROUND OF REFINEMENT. R-FACTOR-ALL CORRESPONDS TO DEPOSITED FILE. R-WORK AND R-FREE FACTORS ARE TAKEN FROM SECOND TO LAST ROUND OF REFINEMENT WHICH USED TEST DATA SET.
RfactorNum. reflection% reflectionSelection details
Rfree0.24003 1966 -RANDOM
Rwork0.1891 ---
all0.19102 19273 --
obs0.19102 19273 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.997 Å2
Baniso -1Baniso -2Baniso -3
1--1.31 Å20 Å20.25 Å2
2---0.07 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 1 191 2156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9512736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.74226.48994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43615382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.457155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021473
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.2984
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21464
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2166
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9541.51273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75622063
X-RAY DIFFRACTIONr_scbond_it3.0473764
X-RAY DIFFRACTIONr_scangle_it4.7744.5673
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.902→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 89 -
Rwork0.236 1047 -
obs-1047 72.26 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.73520.40090.46980.9490.15380.8050.09410.02790.05690.0724-0.07810.11750.01210.0317-0.016-0.02650.0030.005-0.0335-0.0184-0.027534.324129.29060.3632
21.04470.323-0.53872.3846-0.64381.2640.0253-0.0568-0.0465-0.0814-0.1169-0.12470.03870.11190.0916-0.05430.01950.0092-0.01930.0109-0.018545.346110.5617-0.4073
30.77230.118-0.34480.89730.14270.4162-0.03450.02960.0538-0.00830.03530.06110.0122-0.0398-0.0008-0.0297-0.0077-0.01630.0035-0.0082-0.028743.253844.91490.5514
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 832 - 86
2X-RAY DIFFRACTION2BB-1 - 833 - 86
3X-RAY DIFFRACTION3CC-2 - 862 - 89

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