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- PDB-1jpn: GMPPNP Complex of SRP GTPase NG Domain -

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Basic information

Entry
Database: PDB / ID: 1jpn
TitleGMPPNP Complex of SRP GTPase NG Domain
ComponentsSIGNAL RECOGNITION PARTICLE PROTEIN
KeywordsSIGNALING PROTEIN / Ffh / SRP / GMPPNP / Signal Recognition Particle / SRP54 / NG domain
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
ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Signal recognition particle protein
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPadmanabhan, S. / Freymann, D.M.
CitationJournal: Structure / Year: 2001
Title: The conformation of bound GMPPNP suggests a mechanism for gating the active site of the SRP GTPase.
Authors: Padmanabhan, S. / Freymann, D.M.
History
DepositionAug 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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_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_asym_id / _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_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
Remark 99CLOSE CONTACTS THE NINETEEN WATER MOLECULES FLAGGED AS CLOSE CONTACTS (SEE REMARK 500) OCCUPY ...CLOSE CONTACTS THE NINETEEN WATER MOLECULES FLAGGED AS CLOSE CONTACTS (SEE REMARK 500) OCCUPY UNRESOLVED FEATURES OF THE ELECTRON DENSITY MAP THAT HAVE A CHARACTERISTIC "PEANUT" SHAPE. THEY MAY REPRESENT ALTERNATE SOLVENT POSITIONS OR AN UNCHARACTERIZED SOLVENT COMPONENT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,31010
Polymers64,9452
Non-polymers1,3658
Water7,764431
1
B: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1555
Polymers32,4731
Non-polymers6824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: SIGNAL RECOGNITION PARTICLE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1555
Polymers32,4731
Non-polymers6824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.815, 54.531, 99.078
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32472.508 Da / Num. of mol.: 2 / Fragment: NG domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus aquaticus (bacteria) / Plasmid: pET3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O07347
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 29% MPD, 100 mM NaAc, 20mM CaCl2, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120-30 mg/mlprotein1drop
22 mM1dropMgCl2
329 %MPD1reservoir
4100 mMsodium acetate1reservoirpH4.6
520 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 45620 / Num. obs: 45606 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.051 / Rsym value: 0.051
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ffh

1ffh


Resolution: 1.9→15 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.241 3634 random
Rwork0.19 --
obs-44522 -
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 73 440 5117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg0.946
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 40885 / σ(F): 1 / % reflection Rfree: 8 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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