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- PDB-1nnh: Hypothetical protein from Pyrococcus furiosus Pfu-1801964 -

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Basic information

Entry
Database: PDB / ID: 1nnh
TitleHypothetical protein from Pyrococcus furiosus Pfu-1801964
Componentsasparaginyl-tRNA synthetase-related peptide
KeywordsStructural Genomics / Unknown function / Pyrococcus furiosus / asparaginyl-tRNA synthetase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


aminoacyl-tRNA ligase activity / tRNA aminoacylation for protein translation / ATP binding
Similarity search - Function
Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Partial asparaginyl-tRNA synthetase matches COOH terminus
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsTempel, W. / Liu, Z.-J. / Schubot, F.D. / Shah, A. / Arendall III, W.B. / Rose, J.P. / Richardson, D.C. / Richardson, J.S. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Hypothetical protein from Pyrococcus furiosus Pfu-1801964
Authors: Southeast Collaboratory for Structural Genomics
History
DepositionJan 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT IS UNKNOWN.
Remark 6THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M. ...THE PROTEIN WAS CLONED, EXPRESSED AND PURIFIED BY THE SECSG PYROCOCCUS PROTEIN PRODUCTION GROUP (M.W.W.ADAMS, P.S.BRERETON, M.IZUMI, F.E.JENNEY JR., H.-S.LEE, F.L.POOLE II, C.SHAH, F.SUGAR) UNDER THE DIRECTION OF M.W.W.ADAMS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: asparaginyl-tRNA synthetase-related peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1212
Polymers34,0981
Non-polymers231
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: asparaginyl-tRNA synthetase-related peptide
hetero molecules

A: asparaginyl-tRNA synthetase-related peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2424
Polymers68,1962
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565-x,-y+1,z1
Buried area5790 Å2
ΔGint-70 kcal/mol
Surface area21520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.529, 68.529, 150.684
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein asparaginyl-tRNA synthetase-related peptide


Mass: 34098.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TZN6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.53 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 291 K / pH: 9
Details: PEG 550 MME, sodium chloride, bicine, pH 9, modified microbatch, temperature 291K, pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 19, 2002
RadiationMonochromator: SI 220 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 41526 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.039 / Net I/σ(I): 46.8
Reflection shellResolution: 1.65→1.71 Å / Mean I/σ(I) obs: 7.2 / Rsym value: 0.243 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→62.02 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2086 5 %RANDOM
Rwork0.171 ---
obs0.172 41501 100 %-
all-41524 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.65→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2340 0 1 148 2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222414
X-RAY DIFFRACTIONr_bond_other_d00.022246
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9623266
X-RAY DIFFRACTIONr_angle_other_deg3.65735203
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0890.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02513
X-RAY DIFFRACTIONr_nbd_refined0.190.2620
X-RAY DIFFRACTIONr_nbd_other0.2720.22302
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1360.21577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6411.51463
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17122365
X-RAY DIFFRACTIONr_scbond_it1.9423951
X-RAY DIFFRACTIONr_scangle_it3.224.5901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.211 175
Rwork0.178 2900

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