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- PDB-1o87: A new MgGDP complex of the Ffh NG domain -

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Basic information

Entry
Database: PDB / ID: 1o87
TitleA new MgGDP complex of the Ffh NG domain
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsPROTEIN TRANSPORT / FFH / SIGNAL RECOGNITION PARTICLE / SRP / GTPASE / GTP-BINDING / RNA-BINDING
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle protein
Similarity search - Component
Biological speciesTHERMUS AQUATICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsFreymann, D.M.
CitationJournal: Proteins: Struct.,Funct., Genet. / Year: 2004
Title: Novel Protein and Mg2+ Configurations in the Mg2+Gdp Complex of the Srp Gtpase Ffh
Authors: Focia, P.J. / Alam, H. / Lu, T. / Ramirez, U.D. / Freymann, D.M.
History
DepositionNov 25, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2004Provider: 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.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.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_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
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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)66,39214
Polymers65,1432
Non-polymers1,24912
Water4,936274
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1917
Polymers32,5721
Non-polymers6196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2027
Polymers32,5721
Non-polymers6306
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.415, 113.631, 61.382
Angle α, β, γ (deg.)90.00, 111.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.702938, -0.008749, 0.711197), (-0.011637, -0.999932, -0.000799), (0.711155, -0.007715, -0.702992)
Vector: 7.4832, 17.2284, -20.1166)
DetailsCHAIN B WAS TRANSFORMED USING CRYSTALLOGRAPHIC SYMMETRYTO BRING CHAINS B INTO CONTACT WITH CHAIN A AND PLACETHEM IN THE SAME ASYMMETRIC UNIT.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32571.637 Da / Num. of mol.: 2 / Fragment: NG GTPASE 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, 286 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsESSENTIAL FOR EFFICIENT EXPORT OF EXTRA-CYTOPLASMIC PROTEINS. BINDS TO THE SIGNAL SEQUENCE OF ...ESSENTIAL FOR EFFICIENT EXPORT OF EXTRA-CYTOPLASMIC PROTEINS. BINDS TO THE SIGNAL SEQUENCE OF PROTEINS WHEN IT EMERGES FROM THE RIBOSOMES. TWO DOMAIN ARCHITECTURE: NG-DOMAIN BINDS GTP, M-DOMAIN BINDS RNA AND SIGNAL PEPTIDE OF THE PROTEIN TO BE TRANSPORTED. MEMBER OF THE SRP FAMILY OF GTP-BINDING 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: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growpH: 7 / Details: 4.0 M SODIUM FORMATE, pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
132 mg/mlprotein1drop
22 mM1dropMgCl2
32 mMGTP1drop
44 Msodium formate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.96392
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 14, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96392 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 40999 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 24.1
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 6.1 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 6.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRY 1FFH

1ffh


Resolution: 2.1→56.8 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.928 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2023 5.1 %RANDOM
Rwork0.195 ---
obs0.197 38000 97.1 %-
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: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20.45 Å2
2---0.64 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 76 274 4890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214771
X-RAY DIFFRACTIONr_bond_other_d0.0020.024655
X-RAY DIFFRACTIONr_angle_refined_deg1.6692.0276440
X-RAY DIFFRACTIONr_angle_other_deg0.881310744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675605
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_restr0.0870.2727
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02951
X-RAY DIFFRACTIONr_nbd_refined0.2120.21020
X-RAY DIFFRACTIONr_nbd_other0.2430.25344
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2240
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8491.52979
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5824737
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.65431792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5274.51703
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 144
Rwork0.2 2710
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.669

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