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- PDB-3duk: CRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (MFL... -

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Database: PDB / ID: 3duk
TitleCRYSTAL STRUCTURE OF A NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (MFLA_0564) FROM METHYLOBACILLUS FLAGELLATUS KT AT 2.200 A RESOLUTION
ComponentsNTF2-like protein of unknown function
KeywordsUNKNOWN FUNCTION / NTF2-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyPutative lumazine-binding / Putative lumazine-binding / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesMethylobacillus flagellatus KT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of NTF2-like protein of unknown function (YP_544675.1) from METHYLOBACILLUS FLAGELLATUS KT at 2.200 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 17, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NTF2-like protein of unknown function
B: NTF2-like protein of unknown function
C: NTF2-like protein of unknown function
D: NTF2-like protein of unknown function
E: NTF2-like protein of unknown function
F: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,35315
Polymers83,8216
Non-polymers5329
Water3,891216
1
A: NTF2-like protein of unknown function
B: NTF2-like protein of unknown function
C: NTF2-like protein of unknown function
D: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,28911
Polymers55,8814
Non-polymers4087
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9780 Å2
ΔGint-51 kcal/mol
Surface area19060 Å2
MethodPISA
2
E: NTF2-like protein of unknown function
F: NTF2-like protein of unknown function
hetero molecules

E: NTF2-like protein of unknown function
F: NTF2-like protein of unknown function
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1298
Polymers55,8814
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area9280 Å2
ΔGint-42 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.030, 103.030, 130.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (not resid 0:10) and (not resid 90-110) and (not element H)
211chain B and (not resid 0:10) and (not resid 90-110) and (not element H)
112chain A and (not resid 0:10) and (not resid 90-110) and (not element H)
212chain C and (not resid 0:10) and (not resid 90-110) and (not element H)
113chain A and (not resid 0:10) and (not resid 90-110) and (not element H)
213chain D and (not resid 0:10) and (not resid 90-110) and (not element H)
114chain A and (not resid 0:10) and (not resid 90-110) and (not element H)
214chain E and (not resid 0:10) and (not resid 90-110) and (not element H)
115chain A and (not resid 0:10) and (not resid 90-110) and (not element H)
215chain F and (not resid 0:10) and (not resid 90-110) and (not element H)

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
NTF2-like protein of unknown function


Mass: 13970.239 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacillus flagellatus KT (bacteria)
Gene: YP_544675.1, Mfla_0564 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1H3V3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20.0% 2-propanol, 30.0% polyethylene glycol 4000, 0.1M citric acid pH 5.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97932,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 1, 2008 / Details: FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979111
Reflection twinOperator: -h,-k,l / Fraction: 0.295
ReflectionResolution: 2.2→29.981 Å / Num. obs: 41254 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.32 Å2 / Net I/σ(I): 12.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obs% possible all
2.2-2.280.5922.697.6
2.28-2.370.522.999.8
2.37-2.480.4283.599.9
2.48-2.610.334.599.9
2.61-2.770.2545.899.9
2.77-2.980.1698.699.8
2.98-3.280.11212.699.9
3.28-3.760.06320.899.8
3.76-4.720.03831.299.9
4.72-29.980.03135.499.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PHENIXrefinement
SHELXphasing
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.981 Å / σ(F): 1.91 / Phase error: 29 / Stereochemistry target values: TWIN_LSQ_F
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN FULL B FACTORS INCLUDING TLS CONTRIBUTIO 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN FULL B FACTORS INCLUDING TLS CONTRIBUTIO 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. DATA HAS MEROHEDRAL TWINNING WITH THE TWIN OPERATOR (-H,-K,L) AND A REFINED TWIN FRACTION OF 0.295. 5. THE R-FREE SET WAS GENERATED USING THE TWIN LAWS. 6. 1,2-ETHANEDIOL (EDO) WAS MODELED BASED ON CRYOPROTECTANT CONDITIONS. 7. RAMACHANDRAN OUTLIERS ARE LOCATED IN GOOD DENSITY.
RfactorNum. reflection% reflection
Rfree0.2117 2061 5 %
Rwork0.1629 --
obs0.1653 41218 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.427 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 59.48 Å2
Baniso -1Baniso -2Baniso -3
1--19.479 Å20 Å2-0 Å2
2---19.479 Å20 Å2
3----34.278 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5745 0 33 216 5994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311355
X-RAY DIFFRACTIONf_angle_d0.57220385
X-RAY DIFFRACTIONf_dihedral_angle_d11.2672663
X-RAY DIFFRACTIONf_chiral_restr0.045906
X-RAY DIFFRACTIONf_plane_restr0.0021836
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A695X-RAY DIFFRACTIONPOSITIONAL
12B695X-RAY DIFFRACTIONPOSITIONAL0.247
21A694X-RAY DIFFRACTIONPOSITIONAL
22C694X-RAY DIFFRACTIONPOSITIONAL0.219
31A698X-RAY DIFFRACTIONPOSITIONAL
32D698X-RAY DIFFRACTIONPOSITIONAL0.312
41A696X-RAY DIFFRACTIONPOSITIONAL
42E696X-RAY DIFFRACTIONPOSITIONAL0.318
51A699X-RAY DIFFRACTIONPOSITIONAL
52F699X-RAY DIFFRACTIONPOSITIONAL0.222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1998-2.23770.29581000.22041864X-RAY DIFFRACTION98
2.2377-2.27840.24481020.21561928X-RAY DIFFRACTION98
2.2784-2.32220.27231010.2131913X-RAY DIFFRACTION98
2.3222-2.36960.23251030.21631928X-RAY DIFFRACTION98
2.3696-2.42110.30281020.20591958X-RAY DIFFRACTION98
2.4211-2.47740.21841010.19731950X-RAY DIFFRACTION98
2.4774-2.53930.28891000.19911936X-RAY DIFFRACTION98
2.5393-2.60790.22441000.18991942X-RAY DIFFRACTION98
2.6079-2.68460.25951030.19011956X-RAY DIFFRACTION98
2.6846-2.77120.21671050.18521954X-RAY DIFFRACTION98
2.7712-2.87020.2381070.17761952X-RAY DIFFRACTION98
2.8702-2.9850.2081990.16571938X-RAY DIFFRACTION98
2.985-3.12070.24171020.17631971X-RAY DIFFRACTION98
3.1207-3.28510.231980.16391939X-RAY DIFFRACTION98
3.2851-3.49060.20091040.15991980X-RAY DIFFRACTION98
3.4906-3.75970.17061050.14511950X-RAY DIFFRACTION98
3.7597-4.13710.16681080.13041996X-RAY DIFFRACTION98
4.1371-4.73380.14941050.11681988X-RAY DIFFRACTION98
4.7338-5.95640.21171040.13762024X-RAY DIFFRACTION98
5.9564-29.98390.21771100.16542092X-RAY DIFFRACTION98
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)
10.3923-0.4652-0.12181.02170.12220.811-0.0653-0.00680.07250.0594-0.0643-0.11540.157-0.07590.10210.5029-0.00170.01120.43790.00190.4543-4.657743.184844.6015
20.39020.30540.0608-0.57340.15491.2559-0.10440.00560.2088-0.05270.0544-0.0564-0.51670.20830.03190.7108-0.0331-0.00720.4772-0.00640.61084.459675.073643.6763
3-0.8820.4977-0.75890.85660.44362.1269-0.0652-0.0952-0.0414-0.02530.1096-0.2085-0.14850.5871-0.07720.45390.0149-0.01780.6558-0.03990.620916.704359.83650.1327
40.6518-0.6349-0.28111.63940.26040.3135-0.1241-0.07450.03410.18390.0170.03440.0123-0.2060.06970.48190.0189-0.0220.5354-0.0120.4484-16.487458.659350.9013
50.1677-0.07810.31321.0967-0.45351.5044-0.0602-0.2303-0.0720.0420.04610.20160.0119-0.5590.01810.49050.02950.00350.6981-0.01430.507535.024287.85463.111
60.87130.00340.48390.4188-0.50480.387-0.1482-0.14680.14910.0462-0.02670.0218-0.5474-0.26290.1630.63850.1095-0.06050.589-0.03050.447445.171104.720869.2458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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