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- PDB-6anz: Crystal structure of a hypothetical protein from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 6anz
TitleCrystal structure of a hypothetical protein from Neisseria gonorrhoeae
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Neisseria gonorrhoeae / hypothetical protein / uncharacterized protein / iodide phasing / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyUncharacterized protein
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein from Neisseria gonorrhoeae
Authors: Bowatte, K. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0483
Polymers16,8551
Non-polymers1922
Water1,856103
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0956
Polymers33,7112
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
Buried area3880 Å2
ΔGint-56 kcal/mol
Surface area14780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.930, 74.400, 78.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-310-

HOH

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Components

#1: Protein Uncharacterized protein / NegoA.19190.a.B1


Mass: 16855.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: NGK_1889 / Plasmid: NegoA.19190.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B4RQJ2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1743
22.0440
Crystal grow
Temperature (K)Crystal-IDMethodDetailspH
2901vapor diffusion, sitting dropNative protein: Micolytic MCSG1 D8 (1.5 M ammonium sulfate, 100 mM sodium chloride, 100 mM Bis-Tris/HCl, pH 6.5), 25.6 mg/mL NegoA.19190.a.B1.PS38056, cryoprotectant: 25% ethylene glycol, puck MXK4-1, tray 285291d8, I222 crystal form
2892vapor diffusion, sitting dropIodide soak for phasing: RigakuReagents JCSG+ C10 (10% PEG20000, 2% dioxane, 100 mM Bicine/NaOH, pH 9.0), 25.6 mg/mL NegoA.19190.a.B1.PS38056, crystal soaked in 20% ethylene glycol and 2.5 M sodium iodide, then flash frozen, puck ZDJ2-5, tray 285290 c10, P212121 crystal form9

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 21-ID-F10.97872
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RAYONIX MX-3001CCDJun 23, 2017
RIGAKU SATURN 944+2CCDJul 21, 2017
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1diamond(111)SINGLE WAVELENGTHMx-ray1
2Rigaku VarimaxSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978721
21.54181
ReflectionResolution: 1.6→41.459 Å / Num. obs: 19646 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.056 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.063 / Χ2: 1.017 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.645.9050.5922.7814110.8730.64998.7
1.64-1.696.1540.4833.5313920.8830.52899.5
1.69-1.746.0920.3794.5213500.9260.41599.6
1.74-1.796.1060.2965.7113400.9560.32399.7
1.79-1.856.1530.2157.6712770.9810.23599.9
1.85-1.916.1330.1729.612450.9830.18899.8
1.91-1.986.130.12612.7511850.9910.13799.9
1.98-2.076.1270.10215.3311810.9940.11199.8
2.07-2.166.1090.08717.610920.9940.09699.7
2.16-2.266.0830.07620.2110690.9950.083100
2.26-2.396.1320.06722.1210240.9960.073100
2.39-2.536.1130.06124.169460.9970.06699.9
2.53-2.76.1130.05626.039170.9970.06199.8
2.7-2.925.9990.0528.298410.9980.05499.9
2.92-3.26.0280.04730.577880.9980.05199.7
3.2-3.585.9920.04433.377230.9970.048100
3.58-4.135.9330.04334.556300.9980.047100
4.13-5.065.9160.04135.415470.9980.04599.8
5.06-7.165.630.04134.094350.9980.044100
7.16-41.4595.1230.04333.682530.9940.04996.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASER2.7.17phasing
ARPmodel building
Cootmodel building
REFMACrefinement
XDSdata reduction
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.6→41.459 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.13
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1900 9.67 %0
Rwork0.1813 ---
obs0.1842 19645 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.81 Å2 / Biso mean: 30.8044 Å2 / Biso min: 13.05 Å2
Refinement stepCycle: final / Resolution: 1.6→41.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1129 0 10 106 1245
Biso mean--36.99 40.3 -
Num. residues----144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111232
X-RAY DIFFRACTIONf_angle_d1.0811694
X-RAY DIFFRACTIONf_chiral_restr0.078195
X-RAY DIFFRACTIONf_plane_restr0.007221
X-RAY DIFFRACTIONf_dihedral_angle_d13.049761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.640.30151140.2411125199
1.64-1.68440.29321220.2307124799
1.6844-1.73390.28631290.21631255100
1.7339-1.78990.22641380.21851269100
1.7899-1.85390.25341310.20071235100
1.8539-1.92810.23651250.19261273100
1.9281-2.01580.20561480.18811233100
2.0158-2.12210.23781260.17891282100
2.1221-2.25510.21441550.17681237100
2.2551-2.42920.21281300.18721267100
2.4292-2.67360.23071130.19171298100
2.6736-3.06030.20731530.191264100
3.0603-3.85530.19181690.16261272100
3.8553-41.4590.18551470.1663136299
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)
14.06570.70991.61342.51120.2913.98080.0006-0.0296-0.0746-0.26270.00040.22820.1932-0.1789-0.04260.2331-0.02350.03240.12910.04510.182548.912976.975526.5294
26.4139-3.9294-2.21454.9741-1.01083.0978-0.3613-0.26790.29520.30190.3077-0.0978-0.3786-0.0630.05730.2776-0.0042-0.04720.2165-0.01780.149252.307287.465233.1827
39.31630.74484.70852.56160.16494.16930.05430.1828-0.2341-0.11960.01630.18460.1601-0.0117-0.12920.1308-0.00560.01020.1130.00450.143949.478879.84420.4596
44.81252.59133.79613.86961.45553.8927-0.37950.7919-0.0883-0.5550.2624-0.0244-0.23880.32460.13890.2007-0.01010.01670.28240.02080.148254.599882.047814.3724
54.95430.2102-1.45281.95060.42841.4139-0.07280.37050.1772-0.23620.053-0.33-0.09110.10110.00760.1916-0.01350.02450.16590.05170.178260.863487.620217.0339
63.4740.7813-2.38852.87871.43653.0461-0.2656-0.7097-0.80090.8634-0.29790.257-0.1858-0.13270.49380.39720.0226-0.01770.4460.13360.565833.50992.324825.1269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 21 )A-5 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 45 )A22 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 69 )A46 - 69
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 89 )A70 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 131 )A90 - 131
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 138 )A132 - 138

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