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- PDB-2r3s: CRYSTAL STRUCTURE OF A PUTATIVE O-METHYLTRANSFERASE (NPUN_R0239) ... -

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Basic information

Entry
Database: PDB / ID: 2r3s
TitleCRYSTAL STRUCTURE OF A PUTATIVE O-METHYLTRANSFERASE (NPUN_R0239) FROM NOSTOC PUNCTIFORME PCC 73102 AT 2.15 A RESOLUTION
Componentsuncharacterized protein
KeywordsTRANSFERASE / METHYLTRANSFERASE DOMAIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hypothetical RNA methyltransferase / Vaccinia Virus protein VP39 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized protein (ZP_00112478.1) from Nostoc punctiforme PCC 73102 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: 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
Remark 300 BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY ... BIOMOLECULE: 1, 2 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE 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 FOLLOWED BY THE TARGET SEQUENCE. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT DATABASE AT THE TIME OF DEPOSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74214
Polymers74,0512
Non-polymers69212
Water5,549308
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
MethodPISA
2
A: uncharacterized protein
B: uncharacterized protein
hetero molecules

A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,48428
Polymers148,1014
Non-polymers1,38324
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.900, 93.900, 180.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRALA5AA3 - 1554 - 156
21THRALA5BB3 - 1554 - 156
32HISLYS4AA175 - 334176 - 335
42HISLYS4BB175 - 334176 - 335
DetailsCRYSTAL STRUCTURE PACKING SUGGESTS THAT THE BIOLOGICALLY RELEVANT FORM IS A DIMER. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein uncharacterized protein


Mass: 37025.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00112478.1 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.2M Sodium chloride, 1.0M Sodium citrate, 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, 0.97901, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 25, 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
20.979011
30.979251
ReflectionResolution: 2.15→29.696 Å / Num. obs: 44737 / % possible obs: 99.6 % / Redundancy: 7.25 % / Biso Wilson estimate: 34.18 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.35
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2.15-2.230.5962.2532818198.5
2.23-2.320.4792.832432199.9
2.32-2.420.3953.430980199.9
2.42-2.550.3144.433123199.9
2.55-2.710.2385.832544199.9
2.71-2.920.169832708199.9
2.92-3.210.10412.5322611100
3.21-3.670.05521.932585199.9
3.67-4.610.0293732645199.9
4.61-29.6960.02345.232231198.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.696 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.662 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.178
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. THERE IS SOME UNMODELED DENSITY NEAR HIS 242 IN BOTH CHAINS. 5. CL AND ETHYLENE GLYCOL WERE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2245 5 %RANDOM
Rwork0.188 ---
all0.19 ---
obs0.19 44659 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.828 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 42 308 5326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225215
X-RAY DIFFRACTIONr_bond_other_d0.0010.023412
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.9517091
X-RAY DIFFRACTIONr_angle_other_deg0.97238377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2185680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65424.888223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8615830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3231517
X-RAY DIFFRACTIONr_chiral_restr0.0790.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021036
X-RAY DIFFRACTIONr_nbd_refined0.2070.21100
X-RAY DIFFRACTIONr_nbd_other0.1890.23510
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22605
X-RAY DIFFRACTIONr_nbtor_other0.0870.22504
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2314
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2360.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.213
X-RAY DIFFRACTIONr_mcbond_it1.833433
X-RAY DIFFRACTIONr_mcbond_other0.53731328
X-RAY DIFFRACTIONr_mcangle_it2.82655335
X-RAY DIFFRACTIONr_scbond_it4.69382043
X-RAY DIFFRACTIONr_scangle_it6.237111741
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2859MEDIUM POSITIONAL0.290.5
920LOOSE POSITIONAL0.375
2859MEDIUM THERMAL0.992
920LOOSE THERMAL2.3410
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 166 -
Rwork0.234 3013 -
obs-3179 98.42 %
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)
10.64620.4088-0.11560.89510.09150.83020.0642-0.08650.0530.0092-0.0220.0242-0.08950.2224-0.0422-0.017-0.0313-0.0125-0.02750.009-0.1112-19.561-20.983-72.44
20.95230.83810.30581.40590.42421.67170.03720.0369-0.0875-0.0026-0.0206-0.10620.15380.156-0.0166-0.02570.00750.0062-0.05480.0352-0.1277-19.422-39.186-78.966
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA3 - 1364 - 137
22BB2 - 1363 - 137

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