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- PDB-3c0f: Crystal Structure of a novel non-Pfam protein AF1514 from Archeog... -

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Basic information

Entry
Database: PDB / ID: 3c0f
TitleCrystal Structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source
ComponentsUncharacterized protein AF_1514
KeywordsUNKNOWN FUNCTION / hot dog fold / sulphur SAD / methylated
Function / homologyDna Ligase; domain 1 - #340 / Domain of unknown function DUF5619 / Domain of unknown function (DUF5619) / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein AF_1514
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsLi, Y. / Bahti, P. / Shaw, N. / Song, G. / Yin, J. / Zhu, J.-Y. / Zhang, H. / Xu, H. / Wang, B.-C. / Liu, Z.-J.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source.
Authors: Li, Y. / Bahti, P. / Shaw, N. / Song, G. / Chen, S. / Zhang, X. / Zhang, M. / Cheng, C. / Yin, J. / Zhu, J.Y. / Zhang, H. / Che, D. / Xu, H. / Abbas, A. / Wang, B.C. / Liu, Z.J.
History
DepositionJan 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Uncharacterized protein AF_1514


Theoretical massNumber of molelcules
Total (without water)10,6541
Polymers10,6541
Non-polymers00
Water2,180121
1
B: Uncharacterized protein AF_1514

B: Uncharacterized protein AF_1514


Theoretical massNumber of molelcules
Total (without water)21,3082
Polymers21,3082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.737, 49.737, 106.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Uncharacterized protein AF_1514


Mass: 10654.134 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM4304 / Gene: AF1514 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O28758
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium chloride, 0.1 M sodium acetate trihydrate, 10 % v/v MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.5418
ROTATING ANODERIGAKU MICROMAX-00722.29
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV++1IMAGE PLATENov 12, 2007
RIGAKU RAXIS IV++2IMAGE PLATENov 18, 2007
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
22.291
ReflectionResolution: 1.8→45.08 Å / Num. all: 13109 / Num. obs: 11982 / % possible obs: 91.4 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.74 / Redundancy: 9.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.042 / Net I/σ(I): 46.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 4.8 / Num. unique all: 735 / Rsym value: 0.216 / % possible all: 58

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→45.08 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.362 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.8 / σ(I): 1.8 / ESU R: 0.122 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22647 575 4.8 %RANDOM
Rwork0.20554 ---
obs0.20652 11347 91.27 %-
all-13109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.372 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.65 Å20 Å2
3----1.31 Å2
Refine analyzeLuzzati coordinate error obs: 0.035 Å
Refinement stepCycle: LAST / Resolution: 1.8→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms682 0 0 121 803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022699
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.995942
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.217584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.9422534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.34415101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.08154
X-RAY DIFFRACTIONr_chiral_restr0.0580.2102
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02528
X-RAY DIFFRACTIONr_nbd_refined0.1710.2290
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0640.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.20334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.29
X-RAY DIFFRACTIONr_mcbond_it0.281.5434
X-RAY DIFFRACTIONr_mcangle_it0.492669
X-RAY DIFFRACTIONr_scbond_it0.6983308
X-RAY DIFFRACTIONr_scangle_it1.0584.5273
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0.114 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 21 -
Rwork0.409 484 -
obs-420 53.95 %
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)
114.7769-10.246410.317210.4615-7.298512.9779-0.1040.09850.40250.0338-0.1528-0.3771-0.23910.44820.25670.0107-0.03720.02850.106-0.0414-0.011224.89221.687-2.267
231.03410.12427.38034.3188-0.631915.9937-0.2957-0.7735-0.65250.38340.2974-0.2320.67720.2039-0.00170.01990.06610.02480.07150.0028-0.033730.2639.338-5.375
316.8098-3.0384-4.09656.17051.42165.6402-0.0219-0.3261-0.56630.0824-0.07060.04480.33970.27730.09250.0182-0.02590.01020.06740.0125-0.002619.99811.735-5.591
44.4905-0.4854-1.42630.88880.68171.61460.0602-0.1288-0.0752-0.0213-0.0482-0.0574-0.07110.0734-0.0120.0431-0.0111-0.00480.0833-0.00230.014425.57616.617-13.484
516.1165-6.2572-5.538924.815415.481210.80730.37461.09460.9414-1.37590.6344-1.3512-1.35470.8988-1.0090.163-0.00790.06360.1428-0.01130.065332.91823.337-22.959
619.9059-0.0989-0.05824.4325-3.04336.22640.0074-0.02910.5235-0.08460.0577-0.2469-0.5501-0.1468-0.06510.06480.00220.0251-0.0050.0033-0.043325.60523.824-19.472
75.2969-2.54773.06362.978-1.49575.9229-0.20130.24980.1598-0.09080.0328-0.1305-0.40270.12690.16850.0258-0.02960.01980.0576-0.00160.011320.44922.438-12.763
87.13260.20941.85461.25330.01222.9705-0.11020.0545-0.0232-0.04230.08390.1123-0.0842-0.05660.02630.04550.00760.0160.0718-0.02190.012419.16818.344-11.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA3 - 133 - 13
2X-RAY DIFFRACTION2BA14 - 2014 - 20
3X-RAY DIFFRACTION3BA21 - 2921 - 29
4X-RAY DIFFRACTION4BA30 - 5030 - 50
5X-RAY DIFFRACTION5BA51 - 5751 - 57
6X-RAY DIFFRACTION6BA58 - 6458 - 64
7X-RAY DIFFRACTION7BA65 - 7465 - 74
8X-RAY DIFFRACTION8BA75 - 8775 - 87

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