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- PDB-6n7m: 1.78 Angstrom Resolution Crystal Structure of Hypothetical Protei... -

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Basic information

Entry
Database: PDB / ID: 6n7m
Title1.78 Angstrom Resolution Crystal Structure of Hypothetical Protein CD630_05490 from Clostridioides difficile 630.
ComponentsHypothetical Protein CD630_05490
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Hypothetical Protein
Function / homologyUncharacterized protein
Function and homology information
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsMinasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.78 Angstrom Resolution Crystal Structure of Hypothetical Protein CD630_05490 from Clostridioides difficile 630.
Authors: Minasov, G. / Shuvalova, L. / Wawrzak, Z. / Kiryukhina, O. / Dubrovska, I. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical Protein CD630_05490
B: Hypothetical Protein CD630_05490
C: Hypothetical Protein CD630_05490
D: Hypothetical Protein CD630_05490


Theoretical massNumber of molelcules
Total (without water)50,4994
Polymers50,4994
Non-polymers00
Water3,837213
1
A: Hypothetical Protein CD630_05490

B: Hypothetical Protein CD630_05490


Theoretical massNumber of molelcules
Total (without water)25,2502
Polymers25,2502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area8520 Å2
MethodPISA
2
C: Hypothetical Protein CD630_05490

D: Hypothetical Protein CD630_05490


Theoretical massNumber of molelcules
Total (without water)25,2502
Polymers25,2502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area1630 Å2
ΔGint-16 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.620, 58.688, 77.329
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRAA57 - 11731 - 91
21THRTHRBB57 - 11731 - 91
12THRTHRAA57 - 11731 - 91
22THRTHRCC57 - 11731 - 91
13ILEILEAA57 - 11631 - 90
23ILEILEDD57 - 11631 - 90
14ILEILEBB57 - 11831 - 92
24ILEILECC57 - 11831 - 92
15ILEILEBB57 - 11631 - 90
25ILEILEDD57 - 11631 - 90
16ILEILECC57 - 11631 - 90
26ILEILEDD57 - 11631 - 90

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Hypothetical Protein CD630_05490


Mass: 12624.758 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: CD630_05490 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q188Z7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 1.19 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 9.3 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: Classics II (H11), 0.1M Potassium thiocyanate, 30% (w/v) PEG 2000 MME.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.78→46.7 Å / Num. obs: 22345 / % possible obs: 97.74 % / Redundancy: 5.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.048 / Rrim(I) all: 0.113 / Rsym value: 0.102 / Net I/σ(I): 11.1
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1068 / CC1/2: 0.61 / Rpim(I) all: 0.45 / Rrim(I) all: 0.95 / Rsym value: 0.83 / % possible all: 97.89

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→24.52 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.118 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28386 1127 5.1 %RANDOM
Rwork0.24634 ---
obs0.24828 21188 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.866 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20.42 Å2
2---2.96 Å20 Å2
3---1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.78→24.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 0 213 2262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132293
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172183
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6733086
X-RAY DIFFRACTIONr_angle_other_deg0.3961.5995178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7915281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.75727.895114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.11215484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.022505
X-RAY DIFFRACTIONr_gen_planes_other0.0590.02351
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9112.7951094
X-RAY DIFFRACTIONr_mcbond_other3.9072.7911093
X-RAY DIFFRACTIONr_mcangle_it5.1774.1621382
X-RAY DIFFRACTIONr_mcangle_other5.1754.1671383
X-RAY DIFFRACTIONr_scbond_it5.5763.3261199
X-RAY DIFFRACTIONr_scbond_other5.5743.331200
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0444.7851704
X-RAY DIFFRACTIONr_long_range_B_refined9.50734.0682689
X-RAY DIFFRACTIONr_long_range_B_other9.49833.9232653
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A18760.17
12B18760.17
21A20120.09
22C20120.09
31A18470.17
32D18470.17
41B17780.17
42C17780.17
51B17880.1
52D17880.1
61C18320.18
62D18320.18
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 79 -
Rwork0.319 1533 -
obs--98.47 %

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