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- PDB-2rk5: Crystal structure of a domain of the putative hemolysin from Stre... -

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Basic information

Entry
Database: PDB / ID: 2rk5
TitleCrystal structure of a domain of the putative hemolysin from Streptococcus mutans UA159
ComponentsPutative hemolysin
KeywordsTOXIN / Hemolysin / Structural genomics / PSI-2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Membrane / Transmembrane
Function / homology
Function and homology information


flavin adenine dinucleotide binding / membrane => GO:0016020
Similarity search - Function
Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily ...Transporter-associated domain / Transporter associated domain / Transporter associated domain / Cyclin M transmembrane N-terminal domain / CNNM, transmembrane domain / CNNM transmembrane domain profile. / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / CBS domain / CBS domain / CBS domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptococcus mutans UA159 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsZhang, R. / Li, H. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of the putative hemolysin from Streptococcus mutans UA159.
Authors: Zhang, R. / Clancy, S. / Li, H. / Joachimiak, A.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hemolysin


Theoretical massNumber of molelcules
Total (without water)9,8641
Polymers9,8641
Non-polymers00
Water1,802100
1
A: Putative hemolysin

A: Putative hemolysin


Theoretical massNumber of molelcules
Total (without water)19,7282
Polymers19,7282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.490, 40.598, 57.630
Angle α, β, γ (deg.)90.00, 91.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-103-

HOH

21A-107-

HOH

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Components

#1: Protein Putative hemolysin /


Mass: 9863.854 Da / Num. of mol.: 1 / Fragment: Domain: Residues 352-436
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans UA159 (bacteria) / Species: Streptococcus mutans / Strain: UA159 / Serotype c / Gene: hlyX, SMU_1693 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O68574
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.04 Å3/Da / Density % sol: 39.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Hepes pH 7.5, 0.05M MgCl2, 30% PEG MME350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 11, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→57.64 Å / Num. all: 12230 / Num. obs: 12082 / % possible obs: 98.72 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.4
Reflection shellResolution: 1.5→1.539 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 4.3 / % possible all: 92.53

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→57.64 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.109 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23684 625 4.9 %RANDOM
Rwork0.17887 ---
obs0.18182 12082 98.79 %-
all-12082 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20.48 Å2
2--0.75 Å20 Å2
3----0.57 Å2
Refine analyzeLuzzati coordinate error free: 0.055 Å
Refinement stepCycle: LAST / Resolution: 1.5→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 0 100 805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022717
X-RAY DIFFRACTIONr_bond_other_d0.0020.02470
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.953971
X-RAY DIFFRACTIONr_angle_other_deg0.93231157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.734589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.34125.78938
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20615131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.776153
X-RAY DIFFRACTIONr_chiral_restr0.110.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02809
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_nbd_refined0.2520.2152
X-RAY DIFFRACTIONr_nbd_other0.2040.2479
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2374
X-RAY DIFFRACTIONr_nbtor_other0.0840.2392
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.257
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3840.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7471.5565
X-RAY DIFFRACTIONr_mcbond_other0.6771.5180
X-RAY DIFFRACTIONr_mcangle_it2.2832711
X-RAY DIFFRACTIONr_scbond_it4.0563321
X-RAY DIFFRACTIONr_scangle_it5.4054.5260
X-RAY DIFFRACTIONr_rigid_bond_restr2.1093751
X-RAY DIFFRACTIONr_sphericity_free5.089393
X-RAY DIFFRACTIONr_sphericity_bonded3.0783711
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 40 -
Rwork0.21 815 -
obs--92.53 %
Refinement TLS params.Method: refined / Origin x: 11.486 Å / Origin y: 37.748 Å / Origin z: 16.445 Å
111213212223313233
T-0.0113 Å2-0.0033 Å2-0.011 Å2--0.0078 Å20.0026 Å2---0.0233 Å2
L0.7366 °2-0.1722 °2-0.0665 °2-0.4373 °2-0.1698 °2--0.838 °2
S0.0117 Å °0.0318 Å °-0.0117 Å °0.0061 Å °0.0172 Å °0.0189 Å °-0.0094 Å °-0.0199 Å °-0.0289 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 431 - 41
2X-RAY DIFFRACTION1AA44 - 7042 - 68
3X-RAY DIFFRACTION1AA71 - 8869 - 86
4X-RAY DIFFRACTION1AB101 - 2001 - 100

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