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- PDB-3kxa: Crystal Structure of NGO0477 from Neisseria gonorrhoeae -

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Basic information

Entry
Database: PDB / ID: 3kxa
TitleCrystal Structure of NGO0477 from Neisseria gonorrhoeae
ComponentsPutative uncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NGO0477 / Neisseria gonorrhoeae / New protein fold / OPPF / Oxford Protein Production Facility
Function / homology
Function and homology information


Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2240 / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2240 / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ASPARAGINE / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsRen, J. / Sainsbury, S. / Nettleship, J.E. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: Proteins / Year: 2010
Title: The crystal structure of NGO0477 from Neisseria gonorrhoeae reveals a novel protein fold incorporating a helix-turn-helix motif.
Authors: Ren, J. / Sainsbury, S. / Nettleship, J.E. / Saunders, N.J. / Owens, R.J.
History
DepositionDec 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,97343
Polymers63,9844
Non-polymers98939
Water48627
1
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,50422
Polymers31,9922
Non-polymers51220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-38 kcal/mol
Surface area16280 Å2
MethodPISA
2
C: Putative uncharacterized protein
D: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,46921
Polymers31,9922
Non-polymers47719
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-38 kcal/mol
Surface area16290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.823, 124.823, 137.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A5 - 19
2113B5 - 19
3113C5 - 19
4113D5 - 19
1213A26 - 130
2213B26 - 130
3213C26 - 130
4213D26 - 130

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Components

#1: Protein
Putative uncharacterized protein / NGO0477 protein


Mass: 15995.915 Da / Num. of mol.: 4 / Fragment: residues in UNP 13-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: FA1090 / Gene: NGO0477 / Plasmid: OPPF1366 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5F9C2
#2: Chemical
ChemComp-ASN / ASPARAGINE


Type: L-peptide linking / Mass: 132.118 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8N2O3
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 22 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRESIDUES WITH NAME UNX ARE TWO UNKNOWN MOLECULES BOUND TO THE STRUCTURE.

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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 (%)
13.2261.84
2
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris HCl, 22% PEG 400, 0.3M tri-sodium citrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.978
SYNCHROTRONESRF BM1420.90499
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 10, 2006
MARMOSAIC 225 mm CCD2CCDFeb 18, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.904991
ReflectionResolution: 2.8→30 Å / Num. obs: 19515 / % possible obs: 99.7 % / Observed criterion σ(I): -1 / Redundancy: 10.7 % / Biso Wilson estimate: 48.9 Å2 / Rmerge(I) obs: 0.238 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1929 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8→26.31 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / SU B: 24.824 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.982 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27968 1004 5.1 %RANDOM
Rwork0.2298 ---
obs0.23236 18502 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.253 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å21.3 Å20 Å2
2--2.61 Å20 Å2
3----3.91 Å2
Refinement stepCycle: LAST / Resolution: 2.8→26.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 71 27 4160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224182
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.9835620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8425518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.822.874174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.54715792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321544
X-RAY DIFFRACTIONr_chiral_restr0.0710.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213072
X-RAY DIFFRACTIONr_mcbond_it4.74942634
X-RAY DIFFRACTIONr_mcangle_it7.5564240
X-RAY DIFFRACTIONr_scbond_it9.40561548
X-RAY DIFFRACTIONr_scangle_it14.634101380
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A480TIGHT POSITIONAL0.030.05
B480TIGHT POSITIONAL0.030.05
C480TIGHT POSITIONAL0.030.05
D480TIGHT POSITIONAL0.030.05
A459LOOSE POSITIONAL0.065
B459LOOSE POSITIONAL0.055
C459LOOSE POSITIONAL0.055
D459LOOSE POSITIONAL0.055
A480TIGHT THERMAL4.3810.5
B480TIGHT THERMAL4.2610.5
C480TIGHT THERMAL4.5110.5
D480TIGHT THERMAL4.3510.5
A459LOOSE THERMAL5.7430
B459LOOSE THERMAL5.4930
C459LOOSE THERMAL5.3530
D459LOOSE THERMAL5.4930
LS refinement shellResolution: 2.8→2.875 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 76 -
Rwork0.377 1239 -
obs--91.96 %
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)
11.844-0.1284-0.29410.29190.1730.2703-0.0678-0.04470.03430.01150.05560.0196-0.0104-0.01490.01230.10680.0222-0.00220.0456-0.01690.02352.830455.615461.6396
20.6969-0.45660.18151.63340.22910.3120.05750.00150.07280.00030.0518-0.21970.00980.0905-0.10930.09660.0128-0.00460.1267-0.0480.070862.35970.738775.8146
31.217-0.6962-0.51171.18650.04630.33580.01550.0449-0.016-0.0298-0.03230.0367-0.00530.04360.01680.0474-0.02330.01370.08970.01740.014521.768273.704475.9738
42.12030.15840.2220.6923-0.17230.1037-0.01030.00390.28220.00950.04290.0735-0.0425-0.0416-0.03260.12060.01570.04920.13450.03850.094230.020789.383761.745
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 131
2X-RAY DIFFRACTION1B1 - 26
3X-RAY DIFFRACTION1B140
4X-RAY DIFFRACTION1A201 - 211
5X-RAY DIFFRACTION2B27 - 130
6X-RAY DIFFRACTION2A1 - 26
7X-RAY DIFFRACTION2A140
8X-RAY DIFFRACTION3C27 - 131
9X-RAY DIFFRACTION3D1 - 26
10X-RAY DIFFRACTION3D140
11X-RAY DIFFRACTION3C212 - 222
12X-RAY DIFFRACTION4D27 - 130
13X-RAY DIFFRACTION4C1 - 26
14X-RAY DIFFRACTION4C140

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