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- PDB-4a1r: The Structure of Serratia marcescens Lip, a membrane bound compon... -

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Basic information

Entry
Database: PDB / ID: 4a1r
TitleThe Structure of Serratia marcescens Lip, a membrane bound component of the Type VI Secretion System.
ComponentsLIP
KeywordsMEMBRANE PROTEIN / T6SS / BETA-SANDWICH
Function / homologyType VI secretion system, lipoprotein SciN / Type VI secretion system, lipoprotein SciN / Type VI secretion protein SciN-like superfamily / Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113 / Immunoglobulin-like / Sandwich / Mainly Beta / LIP
Function and homology information
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRao, V.A. / Shepherd, S.M. / English, G. / Coulthurst, S.J. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: The Structure of Serratia Marcescens Lip, a Membrane-Bound Component of the Type Vi Secretion System
Authors: Rao, V.A. / Shepherd, S.M. / English, G. / Coulthurst, S.J. / Hunter, W.N.
History
DepositionSep 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Feb 29, 2012Group: Other
Revision 1.3Mar 20, 2013Group: Derived calculations
Revision 1.4May 1, 2024Group: 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 / struct_site
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_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.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_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

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Assembly

Deposited unit
A: LIP
B: LIP
C: LIP
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4476
Polymers65,3624
Non-polymers852
Water6,017334
1
A: LIP


Theoretical massNumber of molelcules
Total (without water)16,3401
Polymers16,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIP


Theoretical massNumber of molelcules
Total (without water)16,3401
Polymers16,3401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3632
Polymers16,3401
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4022
Polymers16,3401
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: LIP
B: LIP


Theoretical massNumber of molelcules
Total (without water)32,6812
Polymers32,6812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-17.1 kcal/mol
Surface area14600 Å2
MethodPISA
6
C: LIP
D: LIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7664
Polymers32,6812
Non-polymers852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-25.4 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.730, 77.750, 54.490
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LIP


Mass: 16340.404 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: DB10 / Plasmid: PET15BTEV_SMLIP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: G5EA77*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsETHAN-1,2-DIOL (EDO): EDO D1176
Sequence detailsGENOME IS NOT YET IN ANY DATABASE

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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: 2.27 Å3/Da / Density % sol: 45 %
Description: THE MODEL USED FOR MOLECULAR REPLACEMENT WAS INITIALLY SOLVED USING SAD. STRUCTURE NOT DEPOSITED IN PDB.
Crystal growDetails: 15 % PEG 3350, 200 MM NACL.

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Data collection

DiffractionMean temperature: 86 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.007
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 13, 2010
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.92→40 Å / Num. obs: 43478 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.6
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL FROM SAD EXPERIMENT

Resolution: 1.92→39.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 5.853 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. C,51-52, D,51-54, B,143-146, C,144-146. RESIDUES WITH WEAK SIDE CHAIN ELECTRON DENSITY HAVE OCCUPANCY SET TO 0.01.
RfactorNum. reflection% reflectionSelection details
Rfree0.29158 2200 5.1 %RANDOM
Rwork0.22036 ---
obs0.22392 41277 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.759 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-1.03 Å2
2---0.7 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.92→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 5 334 4692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9686171
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7895552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31624.11219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34715764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7781533
X-RAY DIFFRACTIONr_chiral_restr0.10.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213476
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.917→1.967 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 147 -
Rwork0.307 2857 -
obs--93.26 %

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