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- PDB-3kk7: Crystal structure of Putative cell invasion protein with MAC/Perf... -

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Basic information

Entry
Database: PDB / ID: 3kk7
TitleCrystal structure of Putative cell invasion protein with MAC/Perforin domain (NP_812351.1) from BACTERIODES THETAIOTAOMICRON VPI-5482 at 2.46 A resolution
ComponentsPutative cell invasion protein with MAC/Perforin domain
KeywordsCELL INVASION / Putative cell invasion protein with MAC/Perforin domain / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Double Stranded RNA Binding Domain - #840 / Nucleotidyltransferase; domain 5 - #400 / Membrane attack complex/perforin (MACPF) domain profile. / MAC/Perforin domain / Membrane attack complex component/perforin (MACPF) domain / Double Stranded RNA Binding Domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MACPF domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of a membrane-attack complex/perforin (MACPF) family protein from the human gut symbiont Bacteroides thetaiotaomicron.
Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C. ...Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Lam, W.W. / Marciano, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Yeh, A. / Zhou, J. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cell invasion protein with MAC/Perforin domain
B: Putative cell invasion protein with MAC/Perforin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,3557
Polymers124,0152
Non-polymers3405
Water4,306239
1
A: Putative cell invasion protein with MAC/Perforin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1674
Polymers62,0071
Non-polymers1603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative cell invasion protein with MAC/Perforin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1883
Polymers62,0071
Non-polymers1802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.400, 127.200, 138.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A36 - 558
2116B36 - 558
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING AND CRYSTAL PACKING SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative cell invasion protein with MAC/Perforin domain


Mass: 62007.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3439 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A267
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 19-558) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 19-558) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY 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: 2.78 Å3/Da / Density % sol: 55.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 5.0000% 2-methyl-2,4-pentanediol, 12.0000% polyethylene glycol 6000, 0.1M HEPES pH 6.7, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97908,0.91837,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.918371
30.979221
ReflectionResolution: 2.46→49.386 Å / Num. obs: 49779 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.436 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.46-2.595.90.7522.34070669030.75294.2
2.59-2.757.30.5463.75062169720.54699.9
2.75-2.947.40.3625.54847865910.36299.8
2.94-3.177.40.228.44510961260.2299.8
3.17-3.477.30.14411.64108756390.14499.8
3.47-3.885.90.13612.12574543680.13684.7
3.88-4.486.90.06519.43087344640.06598.1
4.48-5.497.10.05121.72770339020.05199.9
5.49-7.776.90.05620.62123930560.05699.8
7.77-49.396.30.03626.41100317580.03699

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.25data scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.46→49.386 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.888 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 18.879 / SU ML: 0.19 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.405 / ESU R Free: 0.267
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. (4S)-2-METHY-2,4-PENTANEDIOL (MPD), ETHYLENE GLYCOL (EDO) AND CHLORIDE (CL) MODELED WERE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 2514 5.1 %RANDOM
Rwork0.209 ---
obs0.211 49764 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.81 Å2 / Biso mean: 29.993 Å2 / Biso min: 11.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2---1.35 Å20 Å2
3---1.88 Å2
Refinement stepCycle: LAST / Resolution: 2.46→49.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7998 0 21 239 8258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228249
X-RAY DIFFRACTIONr_bond_other_d0.0020.025530
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.96311189
X-RAY DIFFRACTIONr_angle_other_deg0.914313559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54251012
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40825.285386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.066151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8021524
X-RAY DIFFRACTIONr_chiral_restr0.0860.21230
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021632
X-RAY DIFFRACTIONr_mcbond_it0.5731.55016
X-RAY DIFFRACTIONr_mcbond_other0.1041.52020
X-RAY DIFFRACTIONr_mcangle_it1.09228138
X-RAY DIFFRACTIONr_scbond_it1.67733233
X-RAY DIFFRACTIONr_scangle_it2.6774.53042
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 6582 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.655
LOOSE THERMAL2.5910
LS refinement shellResolution: 2.456→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 158 -
Rwork0.331 3131 -
all-3289 -
obs--88.27 %
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)
13.3869-0.5908-0.94674.39560.18154.32910.41950.11880.48520.1902-0.09010.3745-0.6895-0.1371-0.32930.29680.08630.01320.0333-0.02790.1993-7.336228.602791.0636
20.8660.27610.69530.6010.15971.44350.085-0.0524-0.03420.0388-0.04960.01050.0606-0.0228-0.03540.0132-0.01370.00740.0183-0.01640.02494.7664-1.0925120.4204
34.4348-0.1884-2.16910.98220.30691.70030.14320.42720.3142-0.23910.0105-0.142-0.2109-0.0652-0.15370.20160.03490.04710.09250.03710.04154.8419.320379.2311
40.71350.25920.07813.89590.53442.00310.02240.2640.1555-0.30350.1110.39620.0422-0.4216-0.13340.08620.03-0.07550.23490.07170.1192-13.26918.025187.2272
52.2828-0.01841.17592.06630.38620.7207-0.0835-0.08710.21660.32970.0743-0.19220.02050.04540.00920.14130.08050.0190.2259-0.04590.09872.86544.5855138.8637
61.30740.628-0.63271.5038-0.69560.9605-0.0956-0.0182-0.0723-0.0207-0.0847-0.3860.00780.10220.18030.0097-0.0009-0.00230.03420.0370.113230.572838.7705106.1679
72.6155-1.3377-0.06622.3530.22810.6583-0.07570.02460.0195-0.0368-0.04580.23-0.1037-0.03190.12160.07310.0572-0.01780.0539-0.00090.0494-10.310746.3093125.5267
81.9616-0.48020.16972.78351.17412.3275-0.2401-0.1246-0.29890.33010.19440.29250.16150.04140.04570.07640.05030.07010.03930.04620.07250.540926.408127.0126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 56
2X-RAY DIFFRACTION2A66 - 389
3X-RAY DIFFRACTION3A390 - 493
4X-RAY DIFFRACTION4A494 - 558
5X-RAY DIFFRACTION5B36 - 56
6X-RAY DIFFRACTION6B66 - 389
7X-RAY DIFFRACTION7B390 - 493
8X-RAY DIFFRACTION8B494 - 558

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