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- PDB-2c03: GDP COMPLEX OF SRP GTPASE FFH NG DOMAIN -

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Basic information

Entry
Database: PDB / ID: 2c03
TitleGDP COMPLEX OF SRP GTPASE FFH NG DOMAIN
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsSIGNALING PROTEIN / FFH / GMPPNP / GTP-BINDING / NG DOMAIN / RNA-BINDING / SRP54 NUCLEOTIDE-BINDING / SIGNAL PROTEIN
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
1,4-DIETHYLENE DIOXIDE / GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle protein
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsRamirez, U.D. / Preininger, A.M. / Freymann, D.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Nucleotide-Binding Flexibility in Ultrahigh-Resolution Structures of the Srp Gtpase Ffh
Authors: Ramirez, U.D. / Focia, P.J. / Freymann, D.M.
History
DepositionAug 25, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2May 2, 2012Group: Other
Revision 1.3Oct 16, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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)67,50921
Polymers65,2032
Non-polymers2,30619
Water11,367631
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A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72410
Polymers32,6021
Non-polymers1,1229
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,78611
Polymers32,6021
Non-polymers1,18410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.590, 55.110, 96.110
Angle α, β, γ (deg.)90.00, 101.73, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.873394, 0.008997, -0.486931), (-0.011083, 0.999938, -0.001404), (0.486888, 0.006622, 0.873439)
Vector: 19.4268)

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Components

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


Mass: 32601.660 Da / Num. of mol.: 2 / Fragment: NG, 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
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMANDATORY FOR EFFICIENT EXPORT OF EXTRA-CYTOPLASMIC PROTEINS

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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: 1.5 Å3/Da / Density % sol: 43.9 %
Description: DATA WERE COLLECTED IN TWO OVERLAPPING RESOLUTION RANGES
Crystal growMethod: vapor diffusion, hanging drop / Details: 30% DIOXANE, 2MM GDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.7429
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7429 Å / Relative weight: 1
ReflectionResolution: 1.24→50 Å / Num. obs: 154602 / % possible obs: 94.6 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.24→1.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 96.1

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Processing

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

1ffh


Resolution: 1.24→19.96 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.852 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 9640 7.2 %RANDOM
Rwork0.134 ---
obs0.138 124748 87 %-
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: 21.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.01 Å2
2--0.52 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.24→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 152 631 5342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226170
X-RAY DIFFRACTIONr_bond_other_d0.0020.025991
X-RAY DIFFRACTIONr_angle_refined_deg1.3962.0348407
X-RAY DIFFRACTIONr_angle_other_deg0.802313909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56322.454273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6571588
X-RAY DIFFRACTIONr_chiral_restr0.0760.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027166
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021292
X-RAY DIFFRACTIONr_nbd_refined0.2180.21308
X-RAY DIFFRACTIONr_nbd_other0.1840.26339
X-RAY DIFFRACTIONr_nbtor_refined0.170.22901
X-RAY DIFFRACTIONr_nbtor_other0.0810.23648
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2456
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2710.2211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.274
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0841.55009
X-RAY DIFFRACTIONr_mcbond_other1.8811.51551
X-RAY DIFFRACTIONr_mcangle_it5.66226155
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it9.86832621
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.0444.52252
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: 1.24→1.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 493 -
Rwork0.198 6262 -
obs--78.12 %

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