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- PDB-3c18: Crystal structure of nucleotidyltransferase-like protein (ZP_0053... -

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Basic information

Entry
Database: PDB / ID: 3c18
TitleCrystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from Exiguobacterium sibiricum 255-15 at 1.90 A resolution
ComponentsNucleotidyltransferase-like protein
KeywordsTRANSFERASE / ZP_00538802.1 / nucleotidyltransferase-like protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Nucleotidyltransferase-like domain / YgxA-like, helix-turn-helix domain / Nucleotidyltransferase-like / Helix-turn-helix domain / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Nucleotidyltransferase-like domain / YgxA-like, helix-turn-helix domain / Nucleotidyltransferase-like / Helix-turn-helix domain / Nucleotidyltransferases domain 2 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / :
Similarity search - Component
Biological speciesExiguobacterium sibiricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of nucleotidyltransferase-like protein (ZP_00538802.1) from Exiguobacterium sibiricum 255-15 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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: Nucleotidyltransferase-like protein
B: Nucleotidyltransferase-like protein
C: Nucleotidyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,74610
Polymers103,2713
Non-polymers4757
Water9,692538
1
A: Nucleotidyltransferase-like protein
B: Nucleotidyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2517
Polymers68,8472
Non-polymers4045
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
MethodPISA
2
C: Nucleotidyltransferase-like protein
hetero molecules

C: Nucleotidyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9896
Polymers68,8472
Non-polymers1424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.740, 66.740, 456.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Nucleotidyltransferase-like protein


Mass: 34423.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum (bacteria) / Strain: 255-15 / Gene: ZP_00538802.1, ExigDRAFT_1952 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q41F96, UniProt: B1YK61*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.17
Details: NANODROP, 10.0% PEG 6000, 0.9M Lithium chloride, 0.1M Tris-HCl pH 8.17, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97951
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979511
ReflectionResolution: 1.9→29.709 Å / Num. obs: 95241 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.097 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 9.14
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.5342.25728618305199.7
1.97-2.050.4512.657488180561100
2.05-2.140.3783.155023173401100
2.14-2.250.292455527174101100
2.25-2.390.2245.257441179441100
2.39-2.580.1567.259311184641100
2.58-2.840.1061057412178511100
2.84-3.250.071145695517849199.9
3.25-4.080.04619.95528717720199.9
4.08-29.7090.03423.15535918040199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.709 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.92 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.132
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CL AND GOL WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.233 4765 5 %RANDOM
Rwork0.183 ---
obs0.186 95092 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20.33 Å20 Å2
2--0.66 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7141 0 27 538 7706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0217447
X-RAY DIFFRACTIONr_bond_other_d0.0010.025091
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.95710131
X-RAY DIFFRACTIONr_angle_other_deg1.418312338
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4535912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97122.834374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.002151322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2341573
X-RAY DIFFRACTIONr_chiral_restr0.0770.21145
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028233
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021605
X-RAY DIFFRACTIONr_mcbond_it1.97834398
X-RAY DIFFRACTIONr_mcbond_other0.55331773
X-RAY DIFFRACTIONr_mcangle_it3.35157153
X-RAY DIFFRACTIONr_scbond_it5.59383049
X-RAY DIFFRACTIONr_scangle_it8.326112955
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 350 -
Rwork0.317 6499 -
all-6849 -
obs--99.93 %
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)
10.422-0.1185-0.20210.1241-0.06850.5972-0.05340.0677-0.0190.0047-0.02490.01960.0734-0.14510.0783-0.02660.0050.0457-0.0205-0.0068-0.010711.737554.170631.4677
20.2518-0.17830.0260.3785-0.14720.597-0.02760.10910.0566-0.0708-0.0577-0.0773-0.19840.01180.08530.00580.02490.0187-0.01450.0363-0.058722.426968.788624.3031
30.1138-0.01050.19960.02790.12831.14690.02470.0137-0.01530.0246-0.04920.03520.33040.00540.02460.09250.04230.044-0.11140.00550.02775.765886.891173.4796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2891 - 290
2X-RAY DIFFRACTION2BB0 - 2881 - 289
3X-RAY DIFFRACTION3CC0 - 2881 - 289

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