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- PDB-1vma: Crystal structure of Cell division protein ftsY (TM0570) from The... -

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Basic information

Entry
Database: PDB / ID: 1vma
TitleCrystal structure of Cell division protein ftsY (TM0570) from Thermotoga maritima at 1.60 A resolution
Componentscell division protein FtsY
KeywordsPROTEIN TRANSPORT / TM0570 / CELL DIVISION PROTEIN FTSY / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


: / signal recognition particle binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting / cell division / GTPase activity / GTP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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, nucleotide-binding domain / Signal-recognition particle receptor FtsY / SRP/SRP receptor, N-terminal / 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
CITRIC ACID / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Cell division protein ftsY (TM0570) from Thermotoga maritima at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: cell division protein FtsY
B: cell division protein FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3224
Polymers67,1062
Non-polymers2162
Water7,098394
1
A: cell division protein FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5772
Polymers33,5531
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cell division protein FtsY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7452
Polymers33,5531
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.446, 48.102, 90.792
Angle α, β, γ (deg.)90.00, 107.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein cell division protein FtsY


Mass: 33552.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZ40
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.39 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 277 K / pH: 5
Details: 10.0% PEG-6000, 0.1M Citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034
DetectorType: ADSC / Detector: CCD / Date: Apr 2, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000034 Å / Relative weight: 1
ReflectionResolution: 1.6→24.88 Å / Num. obs: 84144 / % possible obs: 98.8 % / Redundancy: 8.6 % / Biso Wilson estimate: 28.56 Å2 / Rsym value: 0.097 / Net I/σ(I): 18.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 6096 / Rsym value: 0.427 / % possible all: 97.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA(CCP4 4.2)data scaling
MOLREPphasing
REFMAC(5.2.0001)refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1fts

1fts


Resolution: 1.6→24.88 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.645 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 4219 5 %RANDOM
Rwork0.20674 ---
obs0.20905 79919 98.5 %-
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: 21.771 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20.06 Å2
2---0.44 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4408 0 14 394 4816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224529
X-RAY DIFFRACTIONr_bond_other_d0.0010.024396
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9796133
X-RAY DIFFRACTIONr_angle_other_deg0.845310205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.22225.491173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.47415831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0581520
X-RAY DIFFRACTIONr_chiral_restr0.10.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined0.2240.21148
X-RAY DIFFRACTIONr_nbd_other0.1770.24679
X-RAY DIFFRACTIONr_nbtor_other0.0870.22710
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.220
X-RAY DIFFRACTIONr_mcbond_it2.37133009
X-RAY DIFFRACTIONr_mcbond_other0.72331208
X-RAY DIFFRACTIONr_mcangle_it3.20254720
X-RAY DIFFRACTIONr_scbond_it5.10681673
X-RAY DIFFRACTIONr_scangle_it7.219111413
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.21
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 327 5.37 %
Rwork0.253 5765 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.45370.2817-0.1921.7393-0.02711.57820.01960.1676-0.0471-0.3305-0.0606-0.02810.04040.09710.0409-0.04490.0282-0.0006-0.10490.0017-0.17777.7831-0.85351.3226
20.7539-0.1021-0.43832.1553-0.21792.09460.0371-0.097-0.05120.3735-0.04020.4638-0.1511-0.22650.0031-0.08460.00090.0748-0.0567-0.0172-0.0646-7.44071.369326.7954
31.86092.0194-1.83163.44070.86668.3237-0.0310.1066-0.1713-0.2949-0.12960.06710.21480.07570.1606-0.05660.0119-0.035-0.1173-0.0144-0.12710.2483-6.63383.1385
41.4326-0.5131-0.32521.0813-0.16181.75780.0171-0.2845-0.01650.3843-0.0044-0.09160.2071-0.0194-0.01260.1631-0.0387-0.134-0.05910.0053-0.061217.8105-2.066841.7072
50.816-0.0806-0.31871.43070.49662.21810.05080.03970.02710.05350.0773-0.5734-0.03270.275-0.128-0.129-0.0058-0.0417-0.0691-0.0020.107332.85530.550316.1629
61.243-1.314-1.67513.34652.85165.95930.0326-0.2538-0.10830.1565-0.0664-0.01110.45740.24120.03380.21010.0144-0.1834-0.07370.0316-0.00825.0913-8.279739.2181
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 8213 - 94
22AA83 - 28295 - 294
33AA283 - 294295 - 306
44BB1 - 8213 - 94
55BB83 - 28295 - 294
66BB283 - 294295 - 306

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