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- PDB-2obn: Crystal structure of a duf1611 family protein (ava_3511) from ana... -

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Basic information

Entry
Database: PDB / ID: 2obn
TitleCrystal structure of a duf1611 family protein (ava_3511) from anabaena variabilis atcc 29413 at 2.30 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Uncharacterised conserved protein UCP026760 / Domain of unknown function DUF1611, P-loop / Domain of unknown function DUF1611-N, Rossmann-like domain / Domain of unknown function (DUF1611_C) P-loop domain / Domain of unknown function (DUF1611_N) Rossmann-like domain / NAD(P)-binding Rossmann-like Domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized protein
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein of unknown function DUF1611 (YP_324013.1) from Anabaena variabilis ATCC 29413 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: 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
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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. RESIDUE 56 IS MUTATED FROM LYSINE TO TYROSINE. RESIDUE 58 IS MUTATED FROM ASPARTIC ACID TO TYROSINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,35712
Polymers150,2004
Non-polymers1,1578
Water9,386521
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6786
Polymers75,1002
Non-polymers5784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-22 kcal/mol
Surface area26660 Å2
MethodPISA
2
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,6786
Polymers75,1002
Non-polymers5784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-27 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.090, 123.070, 75.210
Angle α, β, γ (deg.)90.000, 103.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNLYSAA6 - 1347 - 135
21ASNLYSBB6 - 1347 - 135
31ASNLYSCC6 - 1347 - 135
41ASNLYSDD6 - 1347 - 135
12GLUASNAA135 - 348136 - 349
22GLUASNBB135 - 348136 - 349
32GLUASNCC135 - 348136 - 349
42GLUASNDD135 - 348136 - 349

NCS ensembles :
ID
1
2

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Components

#1: Protein
Hypothetical protein


Mass: 37549.977 Da / Num. of mol.: 4 / Mutation: K56Y, D58Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: YP_324013.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3M7B8
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.2
Details: 0.2M NaFormate, 20.0% PEG-3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.0000, 0.9806, 0.9805
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 8, 2006
RadiationMonochromator: Single crystal, cylindrically bent, asymmetrically cut Si(220) crystal
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98061
30.98051
ReflectionResolution: 2.3→29.26 Å / Num. obs: 58378 / % possible obs: 93.5 % / Biso Wilson estimate: 40.054 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 9.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.3-2.380.3072.415585970085.6
2.38-2.480.2582.9179361113190.7
2.48-2.590.2083.4168531045691.7
2.59-2.730.184.1180301116393.9
2.73-2.90.1245.6177561099494.7
2.9-3.120.0828.1177431095195.8
3.12-3.430.05811.6180161112095.9
3.43-3.930.04515.1178861110594.5
3.930.0319.5177731105395.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.26 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.344 / SU ML: 0.171 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.379 / ESU R Free: 0.221
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 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.PHOSPHATE ION IS MODELED AROUND RESIDUE 164,165 AND 166 IN EACH SUBUNIT. PEG 400 MOLECULES FROM CRYOPRECTANT ARE MODELED IN EACH SUBUNIT. 5.THERE IS UNKNOWN ELECTRON DENSITY NEAR TO RESIDUE 306 IN EACH SUBUNIT. 6.RESIDUE 84 IN SUBUNIT A, RESIDUE 83 IN SUBUNIT C AND D ARE DISORDERED AND NOT BUILT IN THIS MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.214 2964 5.1 %RANDOM
Rwork0.175 ---
obs0.177 58346 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.889 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å21.42 Å2
2--1.11 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10117 0 72 521 10710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210380
X-RAY DIFFRACTIONr_bond_other_d0.0020.029811
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.97714169
X-RAY DIFFRACTIONr_angle_other_deg0.89322642
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.22651369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99223.867375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.592151576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0491563
X-RAY DIFFRACTIONr_chiral_restr0.0790.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211610
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021915
X-RAY DIFFRACTIONr_nbd_refined0.1920.31976
X-RAY DIFFRACTIONr_nbd_other0.1540.39720
X-RAY DIFFRACTIONr_nbtor_refined0.1650.55090
X-RAY DIFFRACTIONr_nbtor_other0.0830.56013
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.5810
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.384
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.512
X-RAY DIFFRACTIONr_mcbond_it1.0536998
X-RAY DIFFRACTIONr_mcbond_other0.31332821
X-RAY DIFFRACTIONr_mcangle_it1.528510934
X-RAY DIFFRACTIONr_scbond_it2.75883809
X-RAY DIFFRACTIONr_scangle_it4.042113235
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1777MEDIUM POSITIONAL0.370.5
12B1777MEDIUM POSITIONAL0.410.5
13C1777MEDIUM POSITIONAL0.40.5
14D1777MEDIUM POSITIONAL0.430.5
11A1777MEDIUM THERMAL0.382
12B1777MEDIUM THERMAL0.432
13C1777MEDIUM THERMAL0.372
14D1777MEDIUM THERMAL0.392
21A3060MEDIUM POSITIONAL0.370.5
22B3060MEDIUM POSITIONAL0.390.5
23C3060MEDIUM POSITIONAL0.320.5
24D3060MEDIUM POSITIONAL0.360.5
21A3060MEDIUM THERMAL0.572
22B3060MEDIUM THERMAL0.582
23C3060MEDIUM THERMAL0.542
24D3060MEDIUM THERMAL0.582
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 193 -
Rwork0.217 3965 -
obs-4158 95.19 %
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)
12.3401-0.7318-1.0643.1667-0.0845.37340.1557-0.33070.39650.0777-0.0481-0.363-0.45640.6603-0.10760.056-0.08460.02250.0281-0.0724-0.0727-4.6753.729643.0082
21.7256-0.2577-1.23581.8530.16542.48650.2706-0.01280.31780.27140.04050.1437-0.53240.0493-0.3112-0.0358-0.0070.0913-0.2561-0.0194-0.0956-13.629459.470117.2379
31.4518-0.1903-0.7114.73221.35525.9504-0.0585-0.0409-0.35940.33830.16310.10830.37990.0008-0.1046-0.11520.0613-0.0114-0.1797-0.01760.0234-1.698116.716912.5788
41.84820.1535-0.54591.22580.53981.8202-0.07240.1673-0.07530.02370.1285-0.0714-0.07770.2158-0.0561-0.2355-0.0296-0.0205-0.1396-0.062-0.19182.886241.82621.264
51.44190.76230.21255.17121.36886.42470.09150.3458-0.2964-0.1067-0.14840.2730.609-0.41810.05680.1051-0.10860.03940.0371-0.06630.0663-44.57232.754922.2269
62.5853-0.0184-0.31571.08430.51474.20.01110.23910.3345-0.27220.0116-0.0436-0.3519-0.0878-0.0227-0.1558-0.0327-0.026-0.16950.0142-0.0953-38.731828.351431.9444
72.1773-0.1971-0.38015.04292.92376.2192-0.0241-0.4518-0.22790.28230.4533-0.25620.36980.9904-0.42930.0494-0.0354-0.02340.1919-0.0379-0.0622-46.14795.272769.8458
81.4273-0.6328-1.78261.21871.24444.05610.02520.07370.1912-0.0068-0.11190.005-0.0054-0.65270.0867-0.2767-0.027-0.0516-0.0111-0.083-0.121-53.688828.809256.8713
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 1347 - 135
22AA135 - 348136 - 349
33BB6 - 1347 - 135
44BB135 - 348136 - 349
55CC3 - 1344 - 135
66CC135 - 348136 - 349
77DD2 - 1343 - 135
88DD135 - 348136 - 349

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