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- PDB-5dgk: SCCmec type IV Cch - active helicase -

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Basic information

Entry
Database: PDB / ID: 5dgk
TitleSCCmec type IV Cch - active helicase
ComponentsActive helicase
KeywordsREPLICATION / Active ring shaped helicase
Function / homologyDomain of unknown function DUF927 / Domain of unknown function (DUF927) / Cch, helix turn helix domain / Cch helix turn helix domain / helicase activity / nucleotide binding / identical protein binding / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / DUF927 domain-containing protein
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.895 Å
AuthorsRice, P.A. / Mir-Sanchis, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI117593-01 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Staphylococcal SCCmec elements encode an active MCM-like helicase and thus may be replicative.
Authors: Mir-Sanchis, I. / Roman, C.A. / Misiura, A. / Pigli, Y.Z. / Boyle-Vavra, S. / Rice, P.A.
History
DepositionAug 27, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Oct 19, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Active helicase
B: Active helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6916
Polymers136,6302
Non-polymers1,0614
Water30617
1
A: Active helicase
B: Active helicase
hetero molecules

A: Active helicase
B: Active helicase
hetero molecules

A: Active helicase
B: Active helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,07318
Polymers409,8906
Non-polymers3,18312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area38680 Å2
ΔGint-103 kcal/mol
Surface area113630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.140, 110.140, 302.755
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA4 - 556
211chain BB4 - 556

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Components

#1: Protein Active helicase / Uncharacterized protein


Mass: 68314.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: ERS195391_02151, R114_17, R92_17
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q0WXP6
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 32% PEG 200, 0.1M HEPES, pH 7.4 / PH range: 7.4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.89→35.177 Å / Num. obs: 28123 / % possible obs: 92.19 % / Redundancy: 6.8 % / Net I/σ(I): 19
Reflection shellResolution: 2.9→2.95 Å / % possible all: 64.16

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_1839refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.895→35.177 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 2071 7.37 %Random selection
Rwork0.221 26027 --
obs0.224 28098 92.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.34 Å2 / Biso mean: 39.5311 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 2.895→35.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8198 0 88 17 8303
Biso mean--22.48 23.05 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058438
X-RAY DIFFRACTIONf_angle_d0.96311425
X-RAY DIFFRACTIONf_chiral_restr0.0371305
X-RAY DIFFRACTIONf_plane_restr0.0051442
X-RAY DIFFRACTIONf_dihedral_angle_d13.4353047
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6177X-RAY DIFFRACTION5.701TORSIONAL
12B6177X-RAY DIFFRACTION5.701TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.895-2.96210.2621930.22211157125062
2.9621-3.03620.2811040.23351315141970
3.0362-3.11820.25521200.23281487160779
3.1182-3.20990.2871300.23691617174786
3.2099-3.31340.32081480.25121756190492
3.3134-3.43180.27711450.24231814195997
3.4318-3.56910.29421430.24051864200799
3.5691-3.73130.25381500.22391886203699
3.7313-3.92780.24781490.21918622011100
3.9278-4.17350.20071460.223718892035100
4.1735-4.49520.25211490.195818672016100
4.4952-4.94640.23951470.188318962043100
4.9464-5.65960.24091490.217418802029100
5.6596-7.12080.28381510.23618772028100
7.1208-35.17940.26971470.20691860200798
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)
10.970.4290.76810.96180.55160.86110.5330.3356-1.13530.0650.0854-1.04550.3809-0.08070.19250.32030.18410.12070.3614-0.2678-0.674219.569545.1751151.4974
21.37820.26730.05111.656-0.11940.71460.1805-0.22240.4357-0.0107-0.26760.72690.0638-0.05010.04310.0734-0.0013-0.03880.1497-0.02460.457729.561941.5697186.9751
31.2583-0.3699-0.9031-0.04830.10250.6253-0.2099-0.0155-0.68950.3705-0.1387-0.23040.1453-0.04220.23790.4991-0.11310.08410.41180.04630.321512.420338.9371217.1026
41.0275-0.16640.21080.7218-0.40830.4650.14820.1996-1.0687-0.61690.05720.54120.4838-0.3718-0.03170.558-0.1026-0.14820.32760.0542-0.6816-5.404939.2304149.8073
51.6146-0.0884-0.27971.3157-0.09680.6455-0.3186-0.01320.7762-0.03060.3-0.00740.00110.01030.00260.07210.04520.01560.07450.08650.4199-4.744726.6586186.0147
60.0711-0.2866-0.32241.10160.74360.6029-0.1066-0.218-0.51870.2512-0.48890.81020.1064-0.250.43810.4190.0930.05560.4812-0.10420.5082-14.29140.3906216.9481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 141 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 142 through 413 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 414 through 556 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 4 through 128 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 129 through 413 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 414 through 556 )B0

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