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- PDB-5yan: Deconstructing the Salt-Bridge Network of a Computationally Desig... -

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Basic information

Entry
Database: PDB / ID: 5yan
TitleDeconstructing the Salt-Bridge Network of a Computationally Designed Collagen Heterotrimer
Components(Collagen) x 3
KeywordsSTRUCTURAL PROTEIN / Collagen / Heterotrimer / Ion Pairs
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsFan, S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: How electrostatic networks modulate specificity and stability of collagen.
Authors: Zheng, H. / Lu, C. / Lan, J. / Fan, S. / Nanda, V. / Xu, F.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Collagen
B: Collagen
C: Collagen
D: Collagen
E: Collagen
F: Collagen


Theoretical massNumber of molelcules
Total (without water)18,4876
Polymers18,4876
Non-polymers00
Water3,873215
1
A: Collagen
B: Collagen
C: Collagen


Theoretical massNumber of molelcules
Total (without water)9,2443
Polymers9,2443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-19 kcal/mol
Surface area6400 Å2
MethodPISA
2
D: Collagen
E: Collagen
F: Collagen


Theoretical massNumber of molelcules
Total (without water)9,2443
Polymers9,2443
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-18 kcal/mol
Surface area5780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.597, 51.391, 128.522
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Collagen


Mass: 3079.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide Collagen


Mass: 3024.876 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein/peptide Collagen


Mass: 3139.520 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 60% v/v (+/-)-2-methyl-2,4-pentanediol, 40m M sodium cacodylat-etrihydrate at pH 7.0, 80 mM Potassium chloride and 12 mM Sperminetetrahydrochloride.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.77→47.72 Å / Num. obs: 18597 / % possible obs: 98.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 33.21 Å2 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→47.72 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.895 / Rfactor Rfree error: 0.003 / SU R Cruickshank DPI: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.157 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.288 900 4.92 %RANDOM
Rwork0.238 ---
obs0.24 18280 98.1 %-
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.3448 Å20 Å20 Å2
2---4.8822 Å20 Å2
3---10.227 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 1.77→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 0 240 215 1443
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011284HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.111762HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d359SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes30HARMONIC2
X-RAY DIFFRACTIONt_gen_planes180HARMONIC5
X-RAY DIFFRACTIONt_it1284HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion16.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1816SEMIHARMONIC4
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.252 125 4.79 %
Rwork0.234 2487 -
all0.235 2612 -
obs--88.76 %
Refinement TLS params.Method: refined / Origin x: 8.0827 Å / Origin y: -0.3865 Å / Origin z: 14.5302 Å
111213212223313233
T0.376 Å20.0034 Å2-0.0349 Å2-0.2908 Å2-0.0182 Å2--0.1802 Å2
L0 °20.1918 °20.018 °2-0.1291 °20.8723 °2--3.3689 °2
S0.0209 Å °-0.0126 Å °-0.0532 Å °-0.0803 Å °0.0149 Å °-0.0028 Å °-0.0757 Å °0.4037 Å °-0.0358 Å °
Refinement TLS groupSelection details: { *|* }

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