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- PDB-5tup: X-ray Crystal Structure of the Aspergillus fumigatus Sliding Clamp -

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Basic information

Entry
Database: PDB / ID: 5tup
TitleX-ray Crystal Structure of the Aspergillus fumigatus Sliding Clamp
ComponentsProliferating cell nuclear antigen
KeywordsDNA BINDING PROTEIN / sliding clamp
Function / homology
Function and homology information


myosin binding / DNA polymerase processivity factor activity / regulation of DNA replication / membrane => GO:0016020 / DNA replication / DNA binding / nucleus
Similarity search - Function
Myosin-binding domain / Mysoin-binding motif of peroxisomes / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal ...Myosin-binding domain / Mysoin-binding motif of peroxisomes / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesAspergillus fumigatus Z5 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.602 Å
AuthorsBruning, J.B. / Marshall, A.C. / Kroker, A.J. / Wegener, K.L. / Rajapaksha, H.
CitationJournal: FEBS J. / Year: 2017
Title: Structure of the sliding clamp from the fungal pathogen Aspergillus fumigatus (AfumPCNA) and interactions with Human p21.
Authors: Marshall, A.C. / Kroker, A.J. / Murray, L.A. / Gronthos, K. / Rajapaksha, H. / Wegener, K.L. / Bruning, J.B.
History
DepositionNov 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Data collection
Category: diffrn_source / pdbx_struct_assembly_auth_evidence
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen


Theoretical massNumber of molelcules
Total (without water)85,2223
Polymers85,2223
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-14 kcal/mol
Surface area33180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 103.370, 79.200
Angle α, β, γ (deg.)90.000, 96.600, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ILE / End label comp-ID: ILE

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETchain AAA1 - 2542 - 255
2METMETchain BBB1 - 2542 - 255
3GLYGLYchain CCC0 - 2541 - 255
DetailsTrimer as determined by gel filtration

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Components

#1: Protein Proliferating cell nuclear antigen


Mass: 28407.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Z5 (mold) / Gene: Y699_06803 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0J5SJF1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M KCl, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 8, 2015 / Details: Si ans Rh coatings
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→78.68 Å / Num. obs: 27932 / % possible obs: 99.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 55.34 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.076 / Rrim(I) all: 0.204 / Net I/σ(I): 7.2 / Num. measured all: 197392 / Scaling rejects: 93
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.6-2.726.62.01845540.33196.7
9.01-78.686.50.0650.995198.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.85 Å43.94 Å
Translation2.85 Å43.94 Å

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.6phasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CS5

4cs5


Resolution: 2.602→44.024 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1375 4.94 %Random
Rwork0.196 ---
obs0.199 27806 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 220.32 Å2 / Biso mean: 73.7281 Å2 / Biso min: 28.49 Å2
Refinement stepCycle: final / Resolution: 2.602→44.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5613 0 0 183 5796
Biso mean---61.08 -
Num. residues----763
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035686
X-RAY DIFFRACTIONf_angle_d0.7527728
X-RAY DIFFRACTIONf_chiral_restr0.026954
X-RAY DIFFRACTIONf_plane_restr0.004997
X-RAY DIFFRACTIONf_dihedral_angle_d10.1012032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3306X-RAY DIFFRACTION14.158TORSIONAL
12B3306X-RAY DIFFRACTION14.158TORSIONAL
13C3306X-RAY DIFFRACTION14.158TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.602-2.6950.34981470.30782489263694
2.695-2.80290.34391440.28382571271598
2.8029-2.93040.35781370.27052636277399
2.9304-3.08490.30321360.24326592795100
3.0849-3.27810.28721250.228226862811100
3.2781-3.53110.25471230.188226732796100
3.5311-3.88630.2731310.188926452776100
3.8863-4.44810.22851380.17326852823100
4.4481-5.60240.2151540.156326692823100
5.6024-44.03080.2361400.182427182858100
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)
15.1563-0.8966-1.33833.38011.63457.6196-0.03590.4448-0.0769-0.05790.0819-0.1978-0.07841.0663-0.05720.5403-0.13140.0510.5188-0.09190.419224.912625.619627.9051
27.0416-2.1867-0.34986.2984-0.43956.10490.47030.8989-0.2331-1.4434-0.2192-0.0326-0.51331.5027-0.27251.0176-0.15370.01770.9816-0.20630.386425.191323.796514.2897
30.24071.2294-0.97376.4671-5.96775.5189-0.44460.07370.70770.8431-0.7519-1.2568-1.40821.52281.08731.0411-0.26370.00460.7429-0.26420.89926.671431.697439.3969
47.3611-0.8506-1.26614.8567-0.07865.6636-0.4216-0.1053-0.26820.53360.21420.05420.29350.38710.20450.53160.02640.02360.2747-0.00690.401613.29248.498949.0996
55.98440.30260.41396.1372-1.77496.148-0.0312-0.04820.06130.35110.1586-0.16020.39740.8426-0.14230.45510.00720.03820.3396-0.06520.317420.608215.9445.1346
64.26882.4635-0.96134.3806-1.28087.2162-0.12570.26810.07340.28590.18410.14960.2491-0.1368-0.01150.53670.07320.0260.5066-0.00440.3567-11.07223.93810.0157
75.54911.2927-2.26912.00011.01452.34840.32990.70970.51910.38980.10920.5475-0.20050.4455-0.21550.64360.0267-0.04040.98220.05460.3697-11.33465.6738-0.2906
86.59212.77472.60982.44083.69738.31180.02380.4985-0.02820.49130.4145-0.7522-0.16130.7039-0.24780.8709-0.052-0.02710.59670.00230.465214.368721.97134.1734
98.90453.1651.39642.50570.30512.42980.57241.3291-1.4117-1.2642-0.3649-1.99210.38731.3024-0.66780.77110.02060.08910.9264-0.20241.064620.821911.7527-5.4854
107.65012.53311.75832.08113.05397.7343-0.09980.62120.25070.0210.00610.1007-0.07550.163-0.05160.5731-0.0735-0.01890.42690.08170.34284.640217.3909-2.148
116.64330.90864.03381.369-1.62516.9511-0.1783-0.1281-0.21050.1180.02780.1219-0.0932-0.62950.18550.85130.10230.040.3852-0.12230.4272-11.5542-2.386346.3444
127.45490.98423.43682.50391.01973.44110.2291-0.1282-0.1140.0799-0.0951-0.25390.28940.1991-0.11840.6590.04550.05070.3221-0.06420.3572-3.7436-2.135751.4205
136.83047.59594.61358.54275.44053.59090.0986-1.30621.32760.2479-1.031.6171-0.1581-0.84671.07680.79780.10720.26250.6189-0.06690.7669-24.2833-4.596747.001
144.4780.06090.56526.3199-1.6737.1990.14530.4602-0.0501-0.09590.07220.0102-0.08090.1739-0.18830.44380.09960.04730.3711-0.01310.2463-19.5731-8.323925.9386
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 81 )A1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 117 )A82 - 117
3X-RAY DIFFRACTION3chain 'A' and (resid 118 through 134 )A118 - 134
4X-RAY DIFFRACTION4chain 'A' and (resid 135 through 190 )A135 - 190
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 254 )A191 - 254
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 104 )B1 - 104
7X-RAY DIFFRACTION7chain 'B' and (resid 105 through 134 )B105 - 134
8X-RAY DIFFRACTION8chain 'B' and (resid 135 through 182 )B135 - 182
9X-RAY DIFFRACTION9chain 'B' and (resid 183 through 202 )B183 - 202
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 254 )B203 - 254
11X-RAY DIFFRACTION11chain 'C' and (resid 0 through 45 )C0 - 45
12X-RAY DIFFRACTION12chain 'C' and (resid 46 through 117 )C46 - 117
13X-RAY DIFFRACTION13chain 'C' and (resid 118 through 134 )C118 - 134
14X-RAY DIFFRACTION14chain 'C' and (resid 135 through 254 )C135 - 254

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