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- PDB-4fho: Crystal structure of an internalin C2 (inlC2) from Listeria monoc... -

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Basic information

Entry
Database: PDB / ID: 4fho
TitleCrystal structure of an internalin C2 (inlC2) from Listeria monocytogenes str. 4b F2365 at 1.90 A resolution
ComponentsInternalin C2
KeywordsCELL ADHESION/CELL INVASION / leucine rich repeat / N domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / CELL ADHESION-CELL INVASION complex
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta / :
Function and homology information
Biological speciesListeria monocytogenes serotype 4b str. F2365 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an internalin C2 (inlC2) from Listeria monocytogenes str. 4b F2365 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Internalin C2
B: Internalin C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0433
Polymers48,9472
Non-polymers961
Water2,576143
1
A: Internalin C2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5702
Polymers24,4741
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Internalin C2


Theoretical massNumber of molelcules
Total (without water)24,4741
Polymers24,4741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.795, 115.795, 76.927
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Internalin C2


Mass: 24473.674 Da / Num. of mol.: 2 / Fragment: UNP residues 30-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serotype 4b str. F2365 (bacteria)
Strain: F2365 / Gene: inlC2, LMOf2365_0281 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q724E3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 31-260 OF THE TARGET SEQUENCE.

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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: 3.04 Å3/Da / Density % sol: 59.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.00M ammonium sulfate, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.98086
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2012
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98086 Å / Relative weight: 1
ReflectionResolution: 1.9→61.036 Å / Num. all: 42655 / Num. obs: 42655 / % possible obs: 92 % / Redundancy: 5.9 % / Biso Wilson estimate: 37.526 Å2 / Rsym value: 0.08 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-24.30.4971.42736163170.49793.9
2-2.1260.3781.83590759790.37894.1
2.12-2.276.10.2742.43435556390.27493.5
2.27-2.456.10.2132.93167751690.21393.1
2.45-2.696.20.1643.72956847630.16492.2
2.69-36.20.1214.72661842620.12191.6
3-3.476.30.0866.22365637390.08690.6
3.47-4.256.40.0668.21999431320.06689.6
4.25-6.016.40.05210.41554924110.05288.3
6.01-61.0366.30.04213.9782912440.04281.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6U

1h6u


Resolution: 1.9→61.036 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 9.802 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. SULFATE ION (SO4) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 2136 5.1 %RANDOM
Rwork0.1932 ---
obs0.1948 42189 91.14 %-
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 max: 139.27 Å2 / Biso mean: 71.8076 Å2 / Biso min: 43.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å2-0.81 Å20 Å2
2---1.62 Å20 Å2
3---2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 5 143 3523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023453
X-RAY DIFFRACTIONr_bond_other_d0.0040.022123
X-RAY DIFFRACTIONr_angle_refined_deg1.6222.0034750
X-RAY DIFFRACTIONr_angle_other_deg1.50335380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg49.80828.594128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.72615599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.341152
X-RAY DIFFRACTIONr_chiral_restr0.0820.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213798
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02500
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 148 -
Rwork0.335 2825 -
all-2973 -
obs--89.76 %
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)
12.5799-0.2478-0.63733.6141-0.27681.33810.1502-0.4820.57860.46160.2383-0.1190.03550.2075-0.38850.1598-0.01090.08210.1768-0.17750.2832-14.62243.4480.078
22.5790.4114-0.60873.6323-0.75541.00040.08610.54560.4-0.60650.31170.48930.1861-0.1296-0.39780.1961-0.0251-0.09490.23180.17250.2356-26.86437.326-24.545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 260
2X-RAY DIFFRACTION2B34 - 260

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