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- PDB-3gs9: Crystal structure of prophage tail protein gp18 (NP_465809.1) fro... -

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Basic information

Entry
Database: PDB / ID: 3gs9
TitleCrystal structure of prophage tail protein gp18 (NP_465809.1) from Listeria monocytogenes EGD-e at 1.70 A resolution
ComponentsProtein gp18
KeywordsSTRUCTURAL PROTEIN / NP_465809.1 / prophage tail protein gp18 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Phage tail protein beta-alpha-beta fold - #40 / Thrombin, subunit H / Thrombin, subunit H - #10 / Prophage endopeptidase tail, N-terminal / Prophage endopeptidase tail N-terminal domain / Prophage tail endopeptidase / Prophage endopeptidase tail / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Other non-globular ...Phage tail protein beta-alpha-beta fold - #40 / Thrombin, subunit H / Thrombin, subunit H - #10 / Prophage endopeptidase tail, N-terminal / Prophage endopeptidase tail N-terminal domain / Prophage tail endopeptidase / Prophage endopeptidase tail / Phage tail protein beta-alpha-beta fold / 3-Layer(bab) Sandwich / Other non-globular / Special / Alpha Beta
Similarity search - Domain/homology
Protein gp18 [Bacteriophage A118]
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of prophage tail protein gp18 (NP_465809.1) from Listeria monocytogenes EGD-e at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein gp18


Theoretical massNumber of molelcules
Total (without water)40,4321
Polymers40,4321
Non-polymers00
Water6,359353
1
A: Protein gp18

A: Protein gp18

A: Protein gp18


Theoretical massNumber of molelcules
Total (without water)121,2963
Polymers121,2963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6610 Å2
ΔGint-25 kcal/mol
Surface area45900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.575, 135.575, 59.172
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protein gp18


Mass: 40431.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Strain: EGD-e / Serovar 1/2a / Gene: lmo2285, NP_465809.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8Y4Z4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED ...1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. 2. THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.5952.48THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL. THE PHASE RESTRAINTS FROM THAT CRYSTAL WERE USED IN THE CURRENT REFINEMENT.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop4.65NANODROP, 10.0% PEG 1000, 0.20M Lithium sulfate, 0.1M Phosphate-citrate pH 4.65, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop4.36NANODROP, 11.50% PEG 6000, 0.1M Citric acid pH 4.36, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91162
SYNCHROTRONSSRL BL9-220.91162, 0.97975, 0.97956
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDNov 15, 2008Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDDec 7, 2008Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979751
30.979561
ReflectionResolution: 1.7→28.689 Å / Num. obs: 44621 / % possible obs: 100 % / Redundancy: 2.9 % / Biso Wilson estimate: 20.937 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 9.8 / Num. measured all: 128282
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.742.90.4981.8951933200.498100
1.74-1.792.90.4191.8929032250.419100
1.79-1.842.90.3292.2895731180.329100
1.84-1.92.90.272.7874630410.27100
1.9-1.962.90.2273.2854829550.227100
1.96-2.032.90.1784820528490.178100
2.03-2.112.90.1634.2787527290.163100
2.11-2.192.90.1394.9769826710.139100
2.19-2.292.90.1165.7724425180.116100
2.29-2.42.90.1046.4698024100.104100
2.4-2.532.90.0956.7666623160.095100
2.53-2.692.90.0887632521990.088100
2.69-2.872.90.0797.2579820210.079100
2.87-3.12.80.0737.8552719400.073100
3.1-3.42.80.0658.5492417330.065100
3.4-3.82.90.068.8456315880.06100
3.8-4.392.90.0588.2403114060.058100
4.39-5.382.90.0618335011740.061100
5.38-7.62.90.0648.126219080.064100
7.6-28.6892.80.0647.114155000.06498.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→28.689 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 4.127 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.105
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. LYSINES 71,84,182 APPEAR TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WERE MODELED AS LYSINE IN BOTH CHAINS. ALL OTHER LYSINES HAVE BEEN MODELED AS MLY (N-DIMETHYL-LYSINE). 5. CYS27 IS OXIDIZED AS CYSTEINE SULFONIC ACID (OCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2298 5.2 %RANDOM
Rwork0.187 42321 --
obs0.189 44619 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.01 Å2 / Biso mean: 24.197 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.23 Å20 Å2
2---0.47 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2675 0 0 353 3028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222848
X-RAY DIFFRACTIONr_bond_other_d0.0010.021890
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9613895
X-RAY DIFFRACTIONr_angle_other_deg0.8834630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88224.859142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87415.187509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0231513
X-RAY DIFFRACTIONr_chiral_restr0.090.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023154
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02585
X-RAY DIFFRACTIONr_nbd_refined0.2020.2527
X-RAY DIFFRACTIONr_nbd_other0.1920.22026
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21370
X-RAY DIFFRACTIONr_nbtor_other0.0860.21579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.216
X-RAY DIFFRACTIONr_mcbond_it1.97931716
X-RAY DIFFRACTIONr_mcbond_other0.5183675
X-RAY DIFFRACTIONr_mcangle_it2.86652746
X-RAY DIFFRACTIONr_scbond_it4.40581293
X-RAY DIFFRACTIONr_scangle_it5.988111132
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 173 -
Rwork0.24 3135 -
all-3308 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 21.4171 Å / Origin y: 4.4613 Å / Origin z: 24.9861 Å
111213212223313233
T-0.0435 Å2-0.0075 Å20.0132 Å2--0.02 Å20.0139 Å2---0.0239 Å2
L0.3173 °2-0.3466 °20.0062 °2-0.8625 °20.1416 °2--0.1716 °2
S0.0394 Å °0.0262 Å °0.0492 Å °-0.0402 Å °-0.0741 Å °-0.1134 Å °-0.0032 Å °-0.003 Å °0.0347 Å °

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