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- PDB-2qkp: Crystal structure of C-terminal domain of SMU_1151c from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 2qkp
TitleCrystal structure of C-terminal domain of SMU_1151c from Streptococcus mutans
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Domain of unknown function DUF438 / Family of unknown function (DUF438) / PAS domain / Hemerythrin-like / Hemerythrin HHE cation binding domain / PAS domain / Beta-Lactamase / PAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsRamagopal, U.A. / Toro, R. / Gilmore, M. / Wu, B. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of C-terminal domain of SMU_1151c from Streptococcus mutans.
Authors: Ramagopal, U.A. / Toro, R. / Gilmore, M. / Wu, B. / Bain, K. / Gheyi, T. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9807
Polymers70,7644
Non-polymers2163
Water7,873437
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4443
Polymers35,3822
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-27 kcal/mol
Surface area14210 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5364
Polymers35,3822
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-29 kcal/mol
Surface area14280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.999, 53.911, 79.924
Angle α, β, γ (deg.)90.000, 106.050, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit appears to be dimer.

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Components

#1: Protein
Uncharacterized protein


Mass: 17690.898 Da / Num. of mol.: 4 / Fragment: C-terminal domain: residues 315-454
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1151c / Plasmid: BS-pSGX4(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8DU08
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 20% PEG 3000, 0.2M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 63330 / Num. obs: 63330 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.059 / Rsym value: 0.05 / Χ2: 0.687 / Net I/σ(I): 34
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 3.28 / Num. unique all: 11540 / Rsym value: 0.338 / Χ2: 0.46 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.75→29.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.521 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3044 5 %RANDOM
Rwork0.198 ---
all0.2 60316 --
obs0.2 60316 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.743 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0.85 Å2
2--0.79 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4501 0 14 437 4952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224694
X-RAY DIFFRACTIONr_angle_refined_deg1.3471.9536357
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1145559
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50624.651258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3681530
X-RAY DIFFRACTIONr_chiral_restr0.1020.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023672
X-RAY DIFFRACTIONr_nbd_refined0.2060.21921
X-RAY DIFFRACTIONr_nbtor_refined0.310.23243
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2374
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.223
X-RAY DIFFRACTIONr_mcbond_it1.0411.52854
X-RAY DIFFRACTIONr_mcangle_it1.67724526
X-RAY DIFFRACTIONr_scbond_it2.45232058
X-RAY DIFFRACTIONr_scangle_it3.5454.51830
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 220 -
Rwork0.228 4089 -
obs-4309 96.96 %

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