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- PDB-2c04: GMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution -

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Basic information

Entry
Database: PDB / ID: 2c04
TitleGMPPCP complex of SRP GTPase Ffh NG Domain at ultra-high resolution
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsSIGNALING PROTEIN / GMPPNP / GTP-BINDING / RNA-BINDING / SRP / 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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Signal recognition particle protein
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Oct 16, 2019Group: Advisory / Data collection / Other
Category: pdbx_database_status / pdbx_validate_polymer_linkage / reflns_shell
Item: _pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist ..._pdbx_database_status.status_code_sf / _pdbx_validate_polymer_linkage.dist / _pdbx_validate_polymer_linkage.label_alt_id_1 / _pdbx_validate_polymer_linkage.label_alt_id_2 / _reflns_shell.Rmerge_I_obs
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr2_label_alt_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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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)66,2666
Polymers65,1432
Non-polymers1,1234
Water10,539585
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1734
Polymers32,5721
Non-polymers6013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0932
Polymers32,5721
Non-polymers5211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.006, 54.440, 98.831
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.804508, 0.001286, -0.593941), (0.015166, 0.999716, -0.018378), (0.059375, -0.023792, -0.804299)
Vector: 92.1906)

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Components

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


Mass: 32571.637 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-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.51 Å3/Da / Density % sol: 45 %
Description: DATA WERE COLLECTED IN THREE OVERLAPPING RESOLUTION RANGES
Crystal growpH: 4.7
Details: 30% MPD, 0.1M NAACETATE, PH4.7, 20MM CACL2, 0.15M KOACETATE, 2MM MGCL2, 2MM GMPPCP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.15→19.6 Å / Num. obs: 192311 / % possible obs: 94.3 % / Observed criterion σ(I): 3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.7
Reflection shellResolution: 1.15→1.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.4 / % possible all: 90.9

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Processing

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

1jpn


Resolution: 1.15→19.61 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.58 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 13065 7.1 %RANDOM
Rwork0.143 ---
obs0.146 169992 89.8 %-
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: 17.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.44 Å2
2--0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.15→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 66 585 5208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228559
X-RAY DIFFRACTIONr_bond_other_d0.0040.028358
X-RAY DIFFRACTIONr_angle_refined_deg1.4872.03811608
X-RAY DIFFRACTIONr_angle_other_deg0.772319300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52751109
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20622.93372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.466151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.87815107
X-RAY DIFFRACTIONr_chiral_restr0.0670.21312
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029613
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021718
X-RAY DIFFRACTIONr_nbd_refined0.2320.21168
X-RAY DIFFRACTIONr_nbd_other0.1760.26638
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22861
X-RAY DIFFRACTIONr_nbtor_other0.0820.24228
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2508
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0950.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.253
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2570.2204
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2170.263
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0350.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1561.55622
X-RAY DIFFRACTIONr_mcbond_other1.6571.52233
X-RAY DIFFRACTIONr_mcangle_it4.73928613
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.29933347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.7054.52994
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: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 818 -
Rwork0.199 10713 -
obs--80.65 %

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