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- PDB-4n2p: Structure of Archease from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 4n2p
TitleStructure of Archease from Pyrococcus horikoshii
ComponentsProtein archease
KeywordsCHAPERONE / METAL COORDINATION / RNA LIGASE
Function / homology
Function and homology information


tRNA splicing, via endonucleolytic cleavage and ligation / calcium ion binding
Similarity search - Function
Archease, archaea / Archease, Possible Chaperone; Chain: A; domain 1 / Archease domain / Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / 3-Layer(bab) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Protein archease
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.435 Å
AuthorsDesai, K.K. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: A tRNA splicing operon: Archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation.
Authors: Desai, K.K. / Cheng, C.L. / Bingman, C.A. / Phillips Jr., G.N. / Raines, R.T.
History
DepositionOct 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Sep 23, 2020Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein archease
B: Protein archease
C: Protein archease
D: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,50712
Polymers67,8964
Non-polymers6128
Water15,817878
1
A: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1324
Polymers16,9741
Non-polymers1583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2103
Polymers16,9741
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0142
Polymers16,9741
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1513
Polymers16,9741
Non-polymers1772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Protein archease
B: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3427
Polymers33,9482
Non-polymers3955
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-29 kcal/mol
Surface area14170 Å2
MethodPISA
6
C: Protein archease
D: Protein archease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1655
Polymers33,9482
Non-polymers2173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-30 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.219, 55.386, 87.085
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein archease


Mass: 16973.910 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: synthetic gene codon optimized for E. coli, Integrated DNA Technologies
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: PH1536 / Plasmid: pQE70-lacI / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: O59205
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.56 Å3/Da / Density % sol: 52.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium Acetate 0.1 M, 40% MPD, CaCl2 10 mM, MgCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.435→43.95 Å / Num. all: 118858 / Num. obs: 118858 / % possible obs: 94.5 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.01 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.42
Reflection shellResolution: 1.435→1.487 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.7 / % possible all: 94.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
ARP/wARPmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.435→43.946 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 17.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1787 1952 1.69 %
Rwork0.1426 --
obs0.1431 114876 86.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.435→43.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 38 878 5644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014928
X-RAY DIFFRACTIONf_angle_d1.256643
X-RAY DIFFRACTIONf_dihedral_angle_d14.4631894
X-RAY DIFFRACTIONf_chiral_restr0.076716
X-RAY DIFFRACTIONf_plane_restr0.006848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4352-1.45410.2303760.18563523X-RAY DIFFRACTION38
1.4541-1.4740.2034890.17514845X-RAY DIFFRACTION52
1.474-1.49510.2186820.1615420X-RAY DIFFRACTION58
1.4951-1.51740.22141140.15356030X-RAY DIFFRACTION65
1.5174-1.54110.1511130.14386421X-RAY DIFFRACTION69
1.5411-1.56640.19041200.14236948X-RAY DIFFRACTION75
1.5664-1.59340.19251040.14347351X-RAY DIFFRACTION79
1.5934-1.62240.17151640.14017742X-RAY DIFFRACTION83
1.6224-1.65360.1961400.13998025X-RAY DIFFRACTION86
1.6536-1.68740.1951160.14068472X-RAY DIFFRACTION91
1.6874-1.7240.19281340.1428756X-RAY DIFFRACTION93
1.724-1.76420.19371920.13828751X-RAY DIFFRACTION95
1.7642-1.80830.16851680.13358902X-RAY DIFFRACTION95
1.8083-1.85720.17071230.12948979X-RAY DIFFRACTION96
1.8572-1.91180.16311180.13319002X-RAY DIFFRACTION96
1.9118-1.97350.17741980.13128977X-RAY DIFFRACTION97
1.9735-2.04410.16622000.1278976X-RAY DIFFRACTION97
2.0441-2.12590.15151510.12659100X-RAY DIFFRACTION97
2.1259-2.22260.1493510.12549162X-RAY DIFFRACTION98
2.2226-2.33980.16751920.12689099X-RAY DIFFRACTION98
2.3398-2.48640.15081900.13599095X-RAY DIFFRACTION98
2.4864-2.67840.17421960.14569134X-RAY DIFFRACTION98
2.6784-2.94780.19531130.1549247X-RAY DIFFRACTION99
2.9478-3.37430.2072830.14979281X-RAY DIFFRACTION99
3.3743-4.25070.18011920.13869231X-RAY DIFFRACTION99
4.2507-43.96680.19391800.16999135X-RAY DIFFRACTION98

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