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- PDB-6mtz: Crystal structure of an uncharacterized protein from Helicobacter... -

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Basic information

Entry
Database: PDB / ID: 6mtz
TitleCrystal structure of an uncharacterized protein from Helicobacter pylori G27
ComponentsHepC.19480.a.B1
KeywordsUNKNOWN FUNCTION / SSGCID / Structural Genomics / Helicobacter pylori / uncharacterized protein / Seattle Structural Genomics Center for Infectious Disease
Function / homologyDHH phosphoesterase superfamily / IODIDE ION / Uncharacterized protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of an uncharacterized protein from Helicobacter pylori G27
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionOct 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HepC.19480.a.B1
B: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,75043
Polymers82,3672
Non-polymers4,38341
Water5,639313
1
A: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,72524
Polymers41,1831
Non-polymers2,54123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HepC.19480.a.B1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,02519
Polymers41,1831
Non-polymers1,84218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.730, 66.740, 200.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HepC.19480.a.B1


Mass: 41183.301 Da / Num. of mol.: 2 / Fragment: HepyC.19480.a.B11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain G27) (bacteria)
Strain: G27 / Gene: HPG27_386
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: B5Z6F2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytic MCSG1 screen, F3: 200mM Ammonium citrate dibasic pH 5, 20% PEG3350: HepyC.18480.a.B11.PW38477 at 31.62mg/ml. For phasing, a crysta was incubated for 10sec each in reservoir 10% 2. ...Details: Microlytic MCSG1 screen, F3: 200mM Ammonium citrate dibasic pH 5, 20% PEG3350: HepyC.18480.a.B11.PW38477 at 31.62mg/ml. For phasing, a crysta was incubated for 10sec each in reservoir 10% 2.5M NaI in EG and 20% 2.5M NaI in EG (500mM final NaI concentration), and directly vitrified. Tray 301766f3, puck OVZ1-5

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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: Sep 14, 2018
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→44.943 Å / Num. obs: 45317 / % possible obs: 100 % / Redundancy: 13.491 % / Biso Wilson estimate: 39.517 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.101 / Χ2: 1.002 / Net I/σ(I): 17.92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.15-2.218.2850.6063.4932810.8460.647100
2.21-2.2710.8050.5214.7132040.9030.547100
2.27-2.3313.980.4376.431420.9550.453100
2.33-2.414.4070.3777.4230390.9680.39100
2.4-2.4814.4180.3517.9329480.9710.364100
2.48-2.5714.4450.2899.4528820.9810.299100
2.57-2.6714.4390.24111.2427630.9850.25100
2.67-2.7814.4670.18914.0726530.9920.196100
2.78-2.914.430.1616.325720.9940.166100
2.9-3.0414.3880.13518.8324400.9950.14100
3.04-3.2114.3620.10423.6123420.9970.108100
3.21-3.414.2490.08927.4122160.9980.092100
3.4-3.6314.160.07431.6620810.9980.077100
3.63-3.9314.0150.06634.5919790.9990.069100
3.93-4.313.9550.0637.6318000.9990.06299.9
4.3-4.8113.8470.05838.2616460.9990.06100
4.81-5.5513.7750.06235.6114790.9990.06499.9
5.55-6.813.3210.06933.0912540.9980.072100
6.8-9.6212.8340.05337.2110020.9990.05599.8
9.62-44.94311.7190.04939.485940.9990.05197.2

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHASERphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→44.943 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.53
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 2002 4.42 %0
Rwork0.1754 ---
obs0.1777 45246 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 218.14 Å2 / Biso mean: 43.7096 Å2 / Biso min: 14.67 Å2
Refinement stepCycle: final / Resolution: 2.15→44.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5387 0 62 316 5765
Biso mean--56.81 41.99 -
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095540
X-RAY DIFFRACTIONf_angle_d0.7537509
X-RAY DIFFRACTIONf_dihedral_angle_d12.9413259
X-RAY DIFFRACTIONf_chiral_restr0.045827
X-RAY DIFFRACTIONf_plane_restr0.004986
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
2.1501-2.20380.3071440.211130153159
2.2038-2.26340.28811280.202330563184
2.2634-2.330.27831240.191430503174
2.33-2.40520.2321560.182730353191
2.4052-2.49120.27021420.191430473189
2.4912-2.59090.26241310.191830733204
2.5909-2.70880.26221280.186330503178
2.7088-2.85160.23511290.18830933222
2.8516-3.03020.24461300.198731203250
3.0302-3.26410.22521630.18430303193
3.2641-3.59250.21251720.171731023274
3.5925-4.1120.21351380.144831213259
4.112-5.17950.17681660.141731323298
5.1795-44.95250.23761510.19333203471
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)
12.8593-0.48820.38052.81080.19942.13690.09090.15420.2213-0.4094-0.22960.4563-0.5576-0.5470.09860.33050.0971-0.06260.3459-0.05650.284948.812926.353937.5442
20.80950.0203-0.35372.11360.7161.71050.0017-0.05430.0902-0.02590.0543-0.018-0.14320.0541-0.04420.1702-0.01080.00610.17230.01330.14462.362414.653740.5219
32.81251.15510.43824.64091.37254.59180.04040.1566-0.3621-0.4165-0.01740.1980.2898-0.2562-0.0040.32630.0188-0.09380.35820.03590.3546.37043.601213.8881
42.76190.2268-1.09673.4315-0.96743.7316-0.10770.50150.1541-0.1035-0.1055-0.1751-0.23440.28390.17910.2916-0.0552-0.02780.31420.05790.18681.25252.47945.8605
52.93070.6442-0.55743.0301-0.83542.7998-0.17951.08980.0263-0.60430.15560.06280.15150.06580.10390.4085-0.0732-0.01090.5568-0.0090.274778.3701-3.0677-2.6405
62.11160.8260.25882.19921.00662.4693-0.13330.0146-0.0477-0.19750.043-0.03680.13590.09880.06870.19790.03080.02620.16760.04350.221176.3721-2.158423.4614
72.13330.2473-0.92417.7993-0.36426.5290.00490.00260.94070.03320.1294-0.1297-0.58680.1016-0.07910.3335-0.023-0.06190.30590.05490.588986.148225.773420.9134
82.76510.26880.17064.40080.57423.81340.00330.21631.0909-0.03430.10260.7251-0.8821-0.3931-0.15870.73010.11570.03790.48670.14770.853481.042431.796615.414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 96 )A0 - 96
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 245 )A97 - 245
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 347 )A246 - 347
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 51 )B0 - 51
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 133 )B52 - 133
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 245 )B134 - 245
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 291 )B246 - 291
8X-RAY DIFFRACTION8chain 'B' and (resid 292 through 346 )B292 - 346

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