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- PDB-2j46: Water structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution -

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Basic information

Entry
Database: PDB / ID: 2j46
TitleWater structure of T. Aquaticus Ffh NG Domain At 1.1A Resolution
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsNUCLEOTIDE-BINDING / RIBONUCLEOPROTEIN / SRP / FFH / WATER / GTPASE / RNA-BINDING / GTP-BINDING / SIGNAL RECOGNITION PARTICLE
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily ...SRP54, nucleotide-binding domain / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Signal recognition particle protein
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsFreymann, D.M. / Ramirez, U.D.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Analysis of Protein Hydration in Ultra-High Resolution Structures of the Srp Gtpase Ffh
Authors: Ramirez, U.D. / Freymann, D.M.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Structural Basis for Mobility in the 1.1A Crystal Structure of the Ng Domain of T. Aquaticus Ffh
Authors: Ramirez, U.D. / Minasov, G. / Focia, P.J. / Stroud, R. / Walter, P. / Kuhn, P. / Freymann, D.M.
History
DepositionAug 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,74912
Polymers65,1432
Non-polymers60610
Water10,070559
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9107
Polymers32,5721
Non-polymers3396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8395
Polymers32,5721
Non-polymers2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.473, 54.496, 98.799
Angle α, β, γ (deg.)90.00, 97.72, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.80778, 0.054302, 0.586977), (0.037964, 0.998473, -0.040125), (-0.58826, -0.010129, -0.808609)
Vector: 64.5254)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / FIFTY-FOUR HOMOLOG


Mass: 32571.637 Da / Num. of mol.: 2 / Fragment: G DOMAIN, RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS AQUATICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O07347

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Non-polymers , 5 types, 569 molecules

#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.3 Å3/Da / Density % sol: 45.3 %
Crystal growpH: 4.7
Details: 30% MPD, 0.1M NAACETATE, PH 4.7, 0.1M MNCL2, 2MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.785
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.785 Å / Relative weight: 1
ReflectionResolution: 1.1→18.5 Å / Num. obs: 199458 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.6
Reflection shellResolution: 1.1→1.11 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.6 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JPN

1jpn


Resolution: 1.14→29.84 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.163 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: NO WATER HYDROGEN ATOMS ARE INCLUDED I INCLUDED IN THESE COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.172 9676 5 %RANDOM
Rwork0.149 ---
obs0.15 183740 91.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.12 Å2
Refinement stepCycle: LAST / Resolution: 1.14→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4563 0 30 559 5152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225456
X-RAY DIFFRACTIONr_bond_other_d0.0020.025339
X-RAY DIFFRACTIONr_angle_refined_deg1.6212.0117429
X-RAY DIFFRACTIONr_angle_other_deg0.884312356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5545741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08322.541244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3651576
X-RAY DIFFRACTIONr_chiral_restr0.1010.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026383
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021147
X-RAY DIFFRACTIONr_nbd_refined0.2330.21162
X-RAY DIFFRACTIONr_nbd_other0.1840.25324
X-RAY DIFFRACTIONr_nbtor_refined0.170.22655
X-RAY DIFFRACTIONr_nbtor_other0.080.23227
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.243
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.2159
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3791.54546
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.74825572
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.83832204
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.2394.51857
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.14→1.16 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 586
Rwork0.225 11618

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