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- PDB-7r6s: Crystal Structure of the Putative Bacteriophage Protein from Sten... -

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Basic information

Entry
Database: PDB / ID: 7r6s
TitleCrystal Structure of the Putative Bacteriophage Protein from Stenotrophomonas maltophilia
ComponentsPutative bacteriophage protein
KeywordsUNKNOWN FUNCTION / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyProtein of unknown function DUF6696 / X-Tfes, XVIPCD / Glycoside hydrolase, family 19, catalytic / Chitinase class I / chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / Lysozyme-like domain superfamily / Bacteriophage protein
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Brunzelle, J.S. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID)
CitationJournal: Mbio / Year: 2024
Title: Bactericidal effectors of the Stenotrophomonas maltophilia type IV secretion system: functional definition of the nuclease TfdA and structural determination of TfcB.
Authors: Cobe, B.L. / Dey, S. / Minasov, G. / Inniss, N. / Satchell, K.J.F. / Cianciotto, N.P.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative bacteriophage protein
B: Putative bacteriophage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4968
Polymers73,9202
Non-polymers5766
Water5,513306
1
A: Putative bacteriophage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1523
Polymers36,9601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative bacteriophage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3445
Polymers36,9601
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.436, 90.670, 72.067
Angle α, β, γ (deg.)90.000, 103.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative bacteriophage protein


Mass: 36959.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2992 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl-21 Magic / References: UniProt: B2FJG3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein: 8.4mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3; Screen: PEGs II (F6), 0.2M Ammonium sulfate, 0.1M tri-Sodium citrate pH 5.6, 25% (w/v) PEG 4000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97848 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 29, 2021 / Details: Be
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 51491 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 34.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.036 / Rrim(I) all: 0.09 / Rsym value: 0.082 / Χ2: 1.226 / Net I/σ(I): 20.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.928 / Mean I/σ(I) obs: 2 / Num. unique obs: 2592 / CC1/2: 0.705 / CC star: 0.909 / Rpim(I) all: 0.423 / Rrim(I) all: 1.022 / Rsym value: 0.928 / Χ2: 1.01 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→28.71 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.317 / SU ML: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 2591 5.1 %RANDOM
Rwork0.1884 ---
obs0.1905 48349 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.93 Å2 / Biso mean: 44.057 Å2 / Biso min: 22.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0.16 Å2
2--2.56 Å20 Å2
3----1.96 Å2
Refinement stepCycle: final / Resolution: 1.9→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 30 310 5165
Biso mean--65.78 46.64 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0134982
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174682
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6456741
X-RAY DIFFRACTIONr_angle_other_deg0.3331.58310695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7645644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.09421.344320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.14715773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1431558
X-RAY DIFFRACTIONr_chiral_restr0.0580.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.025958
X-RAY DIFFRACTIONr_gen_planes_other0.0460.021250
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 178 -
Rwork0.317 3558 -
all-3736 -
obs--99.28 %
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)
12.3394-0.57361.27845.2065-1.67025.0406-0.01660.29850.0437-0.1357-0.2444-0.2456-0.02620.46940.2610.03430.02730.01590.08790.03650.02434.8433-6.057825.7059
22.4329-0.9111.96641.7869-2.02525.26960.11260.220.01540.1005-0.19290.0991-0.09740.09380.08040.08470.03880.02170.0607-0.00860.0494-9.18059.783116.3259
31.8904-0.41180.18376.27591.00053.86190.30060.1994-0.21710.0499-0.32950.57530.2312-0.41080.02890.09210.0162-0.08520.1051-0.03460.1947-5.6447-7.718322.7194
43.7258-1.08573.91852.1847-1.79747.05740.1220.4061-0.1613-0.2968-0.0879-0.19390.32510.4255-0.03420.12620.10530.04050.1577-0.00940.04038.8213-13.048323.0144
518.6078-4.5128-14.847713.03718.571713.9227-0.1269-0.160.97960.33821.2134-1.02310.25490.6242-1.08640.20340.17040.06080.2791-0.04130.180918.5842-10.761729.9843
62.34151.0187-1.09532.7278-0.68893.27650.0369-0.1123-0.02680.2423-0.1175-0.2489-0.3171-0.0780.08060.0882-0.0546-0.01520.1116-0.01540.059430.1295-22.09762.8805
78.4784.0391-3.74074.5524-2.95736.69490.3545-0.33580.84090.4867-0.22720.3812-1.0114-0.1673-0.12730.20.0256-0.00040.0509-0.05820.101725.3469-14.54659.6861
85.21073.53122.341510.33114.65926.4468-0.00620.09470.0256-0.122-0.24970.46750.0737-0.43330.25590.05590.03930.00410.1016-0.04030.0639-14.7487-2.1517-14.1395
93.0736-1.2823-1.41781.21680.55991.5045-0.0765-0.1066-0.13770.0312-0.06170.06560.0093-00.13820.05110.04940.01010.07760.00210.01663.8954-8.7827-14.997
102.2790.46944.60758.50063.521910.9224-0.23670.44870.288-0.51310.4071-0.841-0.80191.1513-0.17050.0938-0.09710.13060.43010.00660.42025.19137.8275-16.5129
113.9578-3.449-2.83064.50071.9234.44160.04810.26160.1505-0.4508-0.13930.0944-0.25830.00130.09110.28770.0413-0.03160.27370.06050.1482-11.55058.5625-19.0975
121.64-0.9389-2.72431.14440.3168.6493-0.20740.03-0.12040.31870.01560.1260.4019-0.4420.19180.2336-0.11670.04430.17710.01830.1375-22.86820.1185-31.8905
133.7651.84741.46547.28180.3746.4532-0.28280.05650.3028-0.3680.24780.5396-0.1586-0.00940.0350.0412-0.0396-0.03460.10520.05460.1075-26.617821.8899-51.2198
142.69892.2646-0.49092.33170.38083.5048-0.12140.1042-0.3344-0.02030.0397-0.17070.3157-0.07760.08170.0677-0.0703-0.00070.10580.01280.1082-16.464917.3908-46.6943
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 40
2X-RAY DIFFRACTION2A41 - 135
3X-RAY DIFFRACTION3A136 - 172
4X-RAY DIFFRACTION4A173 - 200
5X-RAY DIFFRACTION5A201 - 208
6X-RAY DIFFRACTION6A209 - 294
7X-RAY DIFFRACTION7A295 - 316
8X-RAY DIFFRACTION8B-1 - 13
9X-RAY DIFFRACTION9B14 - 150
10X-RAY DIFFRACTION10B151 - 171
11X-RAY DIFFRACTION11B172 - 203
12X-RAY DIFFRACTION12B204 - 225
13X-RAY DIFFRACTION13B226 - 240
14X-RAY DIFFRACTION14B241 - 316

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