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- PDB-1vk9: CRYSTAL STRUCTURE OF A DUF1893 family protein (TM1506) FROM THERM... -

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Entry
Database: PDB / ID: 1vk9
TitleCRYSTAL STRUCTURE OF A DUF1893 family protein (TM1506) FROM THERMOTOGA MARITIMA AT 2.70 A RESOLUTION
Componentsconserved hypothetical protein TM1506
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


catalytic activity / metal ion binding
Similarity search - Function
Hypothetical protein TM1506 / Protein of unknown function DUF1893, TM1506-like / Hypothetical protein TM1506 / Domain of unknown function (DUF1893) / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / DUF1893 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of an ADP-ribosylated protein with a cytidine deaminase-like fold, but unknown function (TM1506), from Thermotoga maritima at 2.70 A resolution.
Authors: Xu, Q. / Kozbial, P. / McMullan, D. / Krishna, S.S. / Brittain, S.M. / Ficarro, S.B. / DiDonato, M. / Miller, M.D. / Abdubek, P. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Duan, L. / ...Authors: Xu, Q. / Kozbial, P. / McMullan, D. / Krishna, S.S. / Brittain, S.M. / Ficarro, S.B. / DiDonato, M. / Miller, M.D. / Abdubek, P. / Axelrod, H.L. / Chiu, H.J. / Clayton, T. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Han, G.W. / Jaroszewski, L. / Klock, H.E. / Morse, A.T. / Nigoghossian, E. / Paulsen, J. / Reyes, R. / Rife, C.L. / van den Bedem, H. / White, A. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT ...SEQUENCE FOR THE VAL/MET CONFLICT AT RESIDUE 1: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein TM1506
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8268
Polymers17,4341
Non-polymers3927
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: conserved hypothetical protein TM1506
hetero molecules

A: conserved hypothetical protein TM1506
hetero molecules

A: conserved hypothetical protein TM1506
hetero molecules

A: conserved hypothetical protein TM1506
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,30532
Polymers69,7354
Non-polymers1,57028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+2/31
crystal symmetry operation10_665-y+1,-x+1,-z+2/31
Buried area14720 Å2
ΔGint-950 kcal/mol
Surface area25880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)132.891, 132.891, 66.379
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-145-

ZN

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Components

#1: Protein conserved hypothetical protein TM1506


Mass: 17433.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1J4
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 5.06 Å3/Da / Density % sol: 75.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.8
Details: 40% PEG-600, 0.1M Imidazole pH 8.0, 0.2M Zn(OAc)2, pH 5.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796, 1.0332, 0.9795
DetectorType: ADSC / Detector: CCD / Date: Dec 12, 2003
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.03321
30.97951
ReflectionResolution: 2.7→66.38 Å / Num. obs: 9700 / % possible obs: 97.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 75.49 Å2 / Rsym value: 0.086 / Net I/σ(I): 15.7
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 569 / Rsym value: 0.548 / % possible all: 78

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXDphasing
autoSHARPphasing
SOLOMONphasing
REFMAC5.1.24refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.7→57.5 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.772 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.252
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: THERE ARE UNEXPLAINED ELECTRON DENSITY NEAR HIS -5, HIS 0, SER 31, GLU 126, GLU 127. AN UNKNOWN ENTITY WAS PRESENT IN THE ACTIVE SITE, IT MAY CONTAIN FRAGMENTS SUCH AS A SUGAR, A METAL AND A ...Details: THERE ARE UNEXPLAINED ELECTRON DENSITY NEAR HIS -5, HIS 0, SER 31, GLU 126, GLU 127. AN UNKNOWN ENTITY WAS PRESENT IN THE ACTIVE SITE, IT MAY CONTAIN FRAGMENTS SUCH AS A SUGAR, A METAL AND A PHOSPHORYL GROUP, ACCORDING TO DENSITY MAP. THE METALS WERE MODELLED AS ZINC SINCE THE CRYSTAL WAS GROWN IN 0.2M ZINC BUFFER. LYS -7 FROM AN ADJACENT MOLECULE IN THE CRYSTAL IS OBSERVED TO PARTICIPATE IN THE COORDINATION OF ZN 5 IN THE DENSITY MAP. IT IS SUSPICIOUS AND COULD BE AN ARTIFACT OF THE LIMITED RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.25083 465 4.8 %RANDOM
Rwork0.20579 ---
obs0.20789 9155 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.7→57.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 35 9 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211176
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9761577
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5235146
X-RAY DIFFRACTIONr_chiral_restr0.1050.2176
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02846
X-RAY DIFFRACTIONr_nbd_refined0.3120.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.29
X-RAY DIFFRACTIONr_mcbond_it1.7583732
X-RAY DIFFRACTIONr_mcangle_it3.42251177
X-RAY DIFFRACTIONr_scbond_it7.1098444
X-RAY DIFFRACTIONr_scangle_it10.81711400
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.456 52 5.54 %
Rwork0.334 887 -
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)
15.8079-1.4426-0.92932.34520.15551.81690.0888-1.235-0.08780.16230.13790.2366-0.08980.0375-0.22660.1866-0.07280.02250.57880.01660.218717.97762.10437.958
28.87929.686611.94165.70716.19620.3174-0.3049-0.67620.08620.5837-0.07790.0819-0.6669-0.16240.38280.10250.0730.07810.15460.03690.06297.24467.39341.783
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A-10 - 1362 - 148
22H2011

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