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- PDB-4ec6: Ntf2-like, potential transfer protein TraM from Gram-positive con... -

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Basic information

Entry
Database: PDB / ID: 4ec6
TitleNtf2-like, potential transfer protein TraM from Gram-positive conjugative plasmid pIP501
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Gram-positive / conjugation / NTF2-like
Function / homology: / Conjugal transfer protein-like, C-terminal domain / Nuclear Transport Factor 2; Chain: A, - #540 / Nuclear Transport Factor 2; Chain: A, / Roll / membrane / Alpha Beta / Conjugal transfer protein-like C-terminal domain-containing protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsGoessweiner-Mohr, N. / Grumet, L. / Pavkov-Keller, T. / Wang, M. / Keller, W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The 2.5 A Structure of the Enterococcus Conjugation Protein TraM resembles VirB8 Type IV Secretion Proteins.
Authors: Goessweiner-Mohr, N. / Grumet, L. / Arends, K. / Pavkov-Keller, T. / Gruber, C.C. / Gruber, K. / Birner-Gruenberger, R. / Kropec-Huebner, A. / Huebner, J. / Grohmann, E. / Keller, W.
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)114,1126
Polymers114,1126
Non-polymers00
Water7,188399
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)57,0563
Polymers57,0563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative uncharacterized protein
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)57,0563
Polymers57,0563
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,0191
Polymers19,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,0191
Polymers19,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,0191
Polymers19,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)19,0191
Polymers19,0191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0372
Polymers38,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
E: Putative uncharacterized protein
F: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0372
Polymers38,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.210, 54.980, 93.470
Angle α, β, γ (deg.)89.91, 86.44, 78.63
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 214 - 322 / Label seq-ID: 53 - 161

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Putative uncharacterized protein


Mass: 19018.723 Da / Num. of mol.: 6 / Fragment: UNP Residues 214-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Plasmid: pQTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8L1C7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.73 Å3/Da / Density % sol: 28.81 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 7.33
Details: 1 mg/ml protein, 16.5% PEG 3350 (final concentration in drop v/v), 0.1 M Hepes, pH 7.33, microbatch under oil, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2011
Details: toroidal mirror (M2) to vertically and horizontally focus the beam at the sample position (with 2:1 horizontal demagnification)
RadiationMonochromator: BARTELS MONOCROMATOR / Protocol: SAD / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 52900 / Num. obs: 25885 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.116 / Net I/σ(I): 14.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.60.484.05197.7
2.6-2.70.3745.45197.9
2.7-2.790.3355.98197.9
2.79-2.890.2787.26198.2
2.89-30.2149.11198
3-3.120.15411.98198.2
3.12-3.260.13613.61198.6
3.26-3.420.10217.43198.1
3.42-3.60.09818.66196.3
3.6-3.820.08721.77198.4
3.82-4.090.08920.58190.8
4.09-4.410.08323.02192.4
4.41-4.830.05926.95198.9
4.83-5.40.05726.51199.1
5.4-6.240.06224.67199.2
6.24-7.640.06124.85199
7.64-10.80.03339.2199
10.8-500.02651.73198.8

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.36 / FOM acentric: 0.36 / FOM centric: 0 / Reflection: 25883 / Reflection acentric: 25883 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
7.1-46.80.690.6911311131
4.5-7.10.60.634893489
3.6-4.50.550.5542064206
3.1-3.60.420.4244224422
2.7-3.10.220.2277897789
2.5-2.70.120.1248464846

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.13phasing
RESOLVE2.15phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.89 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.859 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.8 / SU ML: 0.22 / SU R Cruickshank DPI: 1.1139 / Cross valid method: THROUGHOUT / ESU R: 1.114 / ESU R Free: 0.325
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26109 1295 5 %RANDOM
Rwork0.20921 ---
obs0.2118 24589 97.87 %-
all-52900 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.803 Å2
Baniso -1Baniso -2Baniso -3
1-2.04 Å2-0.92 Å20.8 Å2
2---0.52 Å2-0.04 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5412 0 0 399 5811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.025526
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9547446
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1395648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36925276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.855151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.121518
X-RAY DIFFRACTIONr_chiral_restr0.120.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT POSITIONAL / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1380.1
12B1380.1
21A1340.13
22C1340.13
31A1280.14
32D1280.14
41A1370.11
42E1370.11
51A1290.14
52F1290.14
61B1340.1
62C1340.1
71B1320.11
72D1320.11
81B1380.09
82E1380.09
91B1330.15
92F1330.15
101C1260.17
102D1260.17
111C1400.14
112E1400.14
121C1290.17
122F1290.17
131D1310.19
132E1310.19
141D1300.15
142F1300.15
151E1350.17
152F1350.17
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 96 -
Rwork0.265 1816 -
obs--97.9 %

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