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- PDB-6okh: Structure of an uncharacterized protein from Leptospira borgpeter... -

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Basic information

Entry
Database: PDB / ID: 6okh
TitleStructure of an uncharacterized protein from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / uncharacterized protein
Function / homologyPutative restriction endonuclease / Nuclease, putative, TT1808 / Putative restriction endonuclease / Restriction endonuclease type II-like / metal ion binding / Putative restriction endonuclease domain-containing protein
Function and homology information
Biological speciesLeptospira borgpetersenii serovar Hardjo-bovis
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Structure of an uncharacterized protein from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5496
Polymers43,4522
Non-polymers974
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-52 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.880, 101.120, 108.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

21A-377-

HOH

31A-427-

HOH

41B-424-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 21725.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197) (bacteria)
Strain: JB197 / Gene: LBJ_2390 / Plasmid: LpboA.19679.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: Q04QG8
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Molecular Dimensions LMB screen, b10: 24 % (v/v) Ethanol 0.1 M HEPES pH 7.8, 40mM Magnesium chloride: LpboA.19679.a.B1.PS38456 at 15mg/ml, incubation at 4C: cryo: 20% EG: tray 308142 b10: ...Details: Molecular Dimensions LMB screen, b10: 24 % (v/v) Ethanol 0.1 M HEPES pH 7.8, 40mM Magnesium chloride: LpboA.19679.a.B1.PS38456 at 15mg/ml, incubation at 4C: cryo: 20% EG: tray 308142 b10: puck kzx0-13. For experimental phasing, a crystal from the same drop was incubated for 20sec in a solution of 80% reservoir and 20% 2.5M Sodium iodide in ethylene glycol, and vitrified: tray: 308142 B10: puck: kzx0-9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 6, 2019
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→45.841 Å / Num. obs: 35536 / % possible obs: 100 % / Redundancy: 10.802 % / Biso Wilson estimate: 30.029 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.045 / Χ2: 0.97 / Net I/σ(I): 37.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.96.0240.5593.425910.9020.613100
1.9-1.956.3140.4094.7225320.9480.446100
1.95-2.016.5650.3036.3624550.9590.329100
2.01-2.077.3560.2448.6523880.9730.263100
2.07-2.148.5110.19411.8223350.9850.207100
2.14-2.219.2550.14816.1922450.9920.156100
2.21-2.299.9370.13218.9921580.9940.139100
2.29-2.3910.7110.1122.920990.9960.115100
2.39-2.4911.7370.126.1620230.9970.105100
2.49-2.6213.5730.08732.0119360.9980.09100
2.62-2.7614.5230.07537.1318200.9990.078100
2.76-2.9314.6360.05845.1817440.9990.06100
2.93-3.1314.6160.04359.14164510.044100
3.13-3.3814.60.03371152910.034100
3.38-3.714.5830.02688.16141810.027100
3.7-4.1414.4810.021107.07127810.02299.8
4.14-4.7814.3170.019123.68114410.01999.9
4.78-5.8514.2790.02110.7197410.02100
5.85-8.2713.8570.022104.377710.02399.9
8.27-45.84112.2110.018129.0344510.01998.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(1.15rc1_3423)refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
PARROTphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.85→45.841 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.69
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 1969 5.54 %0
Rwork0.169 ---
obs0.1708 35529 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.5 Å2 / Biso mean: 30.1709 Å2 / Biso min: 11 Å2
Refinement stepCycle: final / Resolution: 1.85→45.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2792 0 4 319 3115
Biso mean--24.92 39.6 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082975
X-RAY DIFFRACTIONf_angle_d0.8784067
X-RAY DIFFRACTIONf_dihedral_angle_d14.4491833
X-RAY DIFFRACTIONf_chiral_restr0.067459
X-RAY DIFFRACTIONf_plane_restr0.006535
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.85-1.89630.24711360.230523482484
1.8963-1.94750.28361340.204423772511
1.9475-2.00480.23561350.181523742509
2.0048-2.06960.19551400.180123602500
2.0696-2.14350.211140.175324002514
2.1435-2.22930.19491260.16424012527
2.2293-2.33080.18021320.171823992531
2.3308-2.45370.21361420.174423702512
2.4537-2.60740.211430.190723912534
2.6074-2.80870.25711440.189623882532
2.8087-3.09130.21551520.172923942546
3.0913-3.53850.19281470.16524132560
3.5385-4.45750.15021530.142824292582
4.4575-45.85460.19781710.157925162687
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)
14.93452.53555.76081.33792.77876.8992-0.2581-0.34770.7843-0.0691-0.00260.4866-0.3405-0.49120.2440.2410.0458-0.09460.2574-0.01680.34980.929937.060815.9128
23.9898-3.1307-2.07479.25885.18926.11040.11450.11140.1436-0.1696-0.0678-0.6287-0.02660.3109-0.14340.1303-0.02230.02080.21750.07960.214920.944825.389117.0794
34.4537-1.3488-0.25912.67-0.70162.0270.07960.34750.0136-0.392-0.1220.14710.1419-0.18430.00320.2166-0.0560.01320.2199-0.01250.110510.995828.20697.0885
44.5578-1.1060.54312.6439-0.93012.9206-0.04060.4678-0.2868-0.78020.09570.31720.2866-0.1860.03290.2753-0.1038-0.06120.2005-0.00680.16527.616725.3355.9084
54.76910.7806-1.46886.6636-4.0246.1743-0.14880.78930.3347-0.70280.25790.59740.127-0.624-0.18310.3208-0.0504-0.05150.3028-0.00490.20778.607129.20420.8334
66.0251-1.2775-2.95915.69970.15968.45770.1387-0.33060.36440.23660.2546-0.0143-0.61530.0265-0.19270.1643-0.0252-0.01170.15630.00190.13577.770528.300521.0835
71.643-1.1695-0.31683.10960.89582.9716-0.09490.0021-0.2096-0.07580.0240.25120.0307-0.28360.0650.1629-0.07260.00410.17150.00060.14112.112723.153617.2571
83.1424-1.05780.22597.54063.4868.298-0.2794-0.1593-0.00250.32090.2663-0.0785-0.00980.42340.0770.2519-0.05320.00420.18830.03280.15099.229521.197426.692
93.495-0.1361.3441.7674-0.18211.5895-0.0398-0.1023-0.3694-0.0115-0.023-0.03590.362-0.09170.00760.2852-0.06640.03220.16050.01140.20959.863812.920119.158
102.3412-0.3573-1.33873.56913.54083.9888-0.3587-0.5389-0.11740.9285-0.3898-0.78050.00290.71210.45870.4385-0.0271-0.11120.30110.07150.351319.886121.420127.6243
113.91535.72451.49049.81631.86435.3549-0.0538-0.47420.14330.31270.06962.0223-0.3139-0.2138-0.04490.37340.06870.07190.3258-0.01790.659810.98554.736219.9418
120.05240.75280.94045.33486.87898.9060.01560.03220.1206-0.305-0.18850.2593-0.3438-0.07440.24430.23990.0446-0.03830.2431-0.07560.291115.200750.652310.8962
136.495-2.43134.81454.025-2.42588.27120.07370.2231-0.4510.00950.00530.04370.50270.2019-0.12330.1725-0.02340.06330.1152-0.00460.15325.641330.74310.4202
142.43760.2570.21162.73650.13722.14470.0337-0.3595-0.05560.3207-0.1380.09410.04010.08270.07740.2006-0.02920.00970.19840.01520.089824.794639.813721.0256
152.3402-0.75890.05414.60330.07932.6345-0.0552-0.34350.15050.2487-0.0436-0.1705-0.12770.04460.07420.1244-0.03110.00330.1703-0.02530.123726.324144.297721.8882
162.39071.0259-1.44556.9335-1.45746.30050.2893-0.70520.53450.708-0.02810.6639-0.4273-0.1439-0.1610.2643-0.01230.03090.3038-0.04510.206722.171143.734326.8688
172.074-0.6666-0.39653.7503-0.1242.37770.00110.06550.1875-0.18430.0872-0.0953-0.1345-0.011-0.07860.1292-0.04210.00940.12710.01040.114227.63847.62829.1125
184.3673.98434.55266.52114.3764.80160.0320.5779-0.1524-0.2440.2711-0.53260.01490.3333-0.24150.2143-0.05060.06460.2915-0.0030.211932.015741.37012.4104
191.8925-0.817-0.32435.01291.00163.7802-0.0333-0.03620.23630.03770.0616-0.6156-0.02990.5271-0.06120.0979-0.00650.00590.27540.00640.243539.369141.03469.0123
205.47820.49490.71994.5728-0.07882.163-0.26230.7819-1.0491-0.26780.07260.39110.8271-0.1760.29240.3561-0.00080.06610.3256-0.0620.320729.75329.29421.5526
216.55833.76560.02628.10283.08255.4886-0.71081.12161.9088-1.16660.7121-0.547-0.4901-0.1333-0.01310.4163-0.0757-0.10670.46790.2230.6931-1.270441.0426.3182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 21 through 35 )B21 - 35
2X-RAY DIFFRACTION2chain 'B' and (resid 36 through 56 )B36 - 56
3X-RAY DIFFRACTION3chain 'B' and (resid 57 through 71 )B57 - 71
4X-RAY DIFFRACTION4chain 'B' and (resid 72 through 90 )B72 - 90
5X-RAY DIFFRACTION5chain 'B' and (resid 91 through 101 )B91 - 101
6X-RAY DIFFRACTION6chain 'B' and (resid 102 through 112 )B102 - 112
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 135 )B113 - 135
8X-RAY DIFFRACTION8chain 'B' and (resid 136 through 145 )B136 - 145
9X-RAY DIFFRACTION9chain 'B' and (resid 146 through 170 )B146 - 170
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 180 )B171 - 180
11X-RAY DIFFRACTION11chain 'A' and (resid 4 through 20 )A4 - 20
12X-RAY DIFFRACTION12chain 'A' and (resid 21 through 35 )A21 - 35
13X-RAY DIFFRACTION13chain 'A' and (resid 36 through 55 )A36 - 55
14X-RAY DIFFRACTION14chain 'A' and (resid 56 through 71 )A56 - 71
15X-RAY DIFFRACTION15chain 'A' and (resid 72 through 90 )A72 - 90
16X-RAY DIFFRACTION16chain 'A' and (resid 91 through 101 )A91 - 101
17X-RAY DIFFRACTION17chain 'A' and (resid 102 through 135 )A102 - 135
18X-RAY DIFFRACTION18chain 'A' and (resid 136 through 145 )A136 - 145
19X-RAY DIFFRACTION19chain 'A' and (resid 146 through 170 )A146 - 170
20X-RAY DIFFRACTION20chain 'A' and (resid 171 through 181 )A171 - 181
21X-RAY DIFFRACTION21chain 'B' and (resid 5 through 20 )B5 - 20

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