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- PDB-2p7i: CRYSTAL STRUCTURE OF a SAM dependent methyl-transferase type 12 f... -

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Basic information

Entry
Database: PDB / ID: 2p7i
TitleCRYSTAL STRUCTURE OF a SAM dependent methyl-transferase type 12 family protein (ECA1738) FROM PECTOBACTERIUM ATROSEPTICUM SCRI1043 AT 1.74 A RESOLUTION
ComponentsHypothetical protein
KeywordsTRANSFERASE / PUTATIVE METHYLTRANSFERASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyMethyltransferase domain / Vaccinia Virus protein VP39 / transferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Methyltransferase
Function and homology information
Biological speciesPectobacterium atrosepticum SCRI1043 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_049838.1) from Erwinia carotovora atroseptica SCRI1043 at 1.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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_asym_id / _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.ptnr3_auth_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_asym_id / _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_asym_id / _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 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.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7927
Polymers57,3712
Non-polymers4215
Water6,593366
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,58514
Polymers114,7434
Non-polymers84210
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area11790 Å2
ΔGint-49 kcal/mol
Surface area34300 Å2
MethodPISA
2
A: Hypothetical protein
B: Hypothetical protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)462,33856
Polymers458,97116
Non-polymers3,36740
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_654-x+1,y,-z-11
crystal symmetry operation6_564x,-y+1,-z-11
crystal symmetry operation7_554y,x,-z-11
crystal symmetry operation8_664-y+1,-x+1,-z-11
Buried area57750 Å2
ΔGint-245 kcal/mol
Surface area126620 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.830, 120.830, 149.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-250-

CL

21A-254-

HOH

31A-364-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: A B)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Refine code: 4

Component-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNGLYAA22 - 24623 - 247
2TYRGLNBB21 - 24922 - 250

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical protein /


Mass: 28685.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum SCRI1043 (bacteria)
Species: Pectobacterium atrosepticum / Strain: SCRI 1043 / Gene: YP_049838.1, ECA1738 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6D6E7

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Non-polymers , 5 types, 371 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 64.4% 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.5, 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: 0.97899, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 2, 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
10.978991
20.979251
ReflectionResolution: 1.74→29.111 Å / Num. obs: 56875 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.14 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.3
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.797.40.73065841691.108100
1.79-1.837.40.82999840640.905100
1.83-1.897.41.22891439200.663100
1.89-1.957.41.42817938220.536100
1.95-2.017.422758037300.376100
2.01-2.087.42.52645835760.308100
2.08-2.167.43.22585635000.238100
2.16-2.257.43.72469033310.202100
2.25-2.357.44.42385332260.17100
2.35-2.467.45.12282830820.144100
2.46-2.597.45.62179729560.127100
2.59-2.757.45.92042827670.116100
2.75-2.947.46.41935326320.102100
2.94-3.187.37.61799424530.082100
3.18-3.487.310.21657322610.061100
3.48-3.897.313.11499720560.048100
3.89-4.497.313.81328918290.045100
4.49-5.57.214.41125515690.041100
5.5-7.78714.4864512410.043100
7.78-29.116.417.444226910.03696.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.3.0034refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→29.111 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 4.556 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.088
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TRS, CL, NA AND MPD ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 5. THE N-TERMINAL RESIDUES 0-21 FOR CHAIN A, AND 0-20 FOR CHAIN B ARE DISORDERED. 6. RAMACHANDRAN OUTLIERS FOR RESIDUE 199 ARE SUPPORTED BY UNAMBIGUOUS ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2883 5.1 %RANDOM
Rwork0.155 ---
all0.156 ---
obs0.156 56875 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.628 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2--1.35 Å20 Å2
3----2.69 Å2
Refinement stepCycle: LAST / Resolution: 1.74→29.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 26 366 4008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223859
X-RAY DIFFRACTIONr_bond_other_d0.0010.022619
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9435261
X-RAY DIFFRACTIONr_angle_other_deg0.936340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52823.35203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21215631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7781532
X-RAY DIFFRACTIONr_chiral_restr0.0910.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02872
X-RAY DIFFRACTIONr_nbd_refined0.2160.2722
X-RAY DIFFRACTIONr_nbd_other0.1980.22890
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21869
X-RAY DIFFRACTIONr_nbtor_other0.0870.22116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2270
X-RAY DIFFRACTIONr_metal_ion_refined0.1090.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0670.22
X-RAY DIFFRACTIONr_mcbond_it1.73432326
X-RAY DIFFRACTIONr_mcbond_other0.713941
X-RAY DIFFRACTIONr_mcangle_it2.82953758
X-RAY DIFFRACTIONr_scbond_it4.69281568
X-RAY DIFFRACTIONr_scangle_it6.885111482
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2916 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.290.5
BMEDIUM THERMAL1.332
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 212 -
Rwork0.26 3957 -
obs-4169 100 %
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)
10.4943-0.2857-0.07410.4046-0.05281.0753-0.0683-0.06530.04760.06180.0446-0.0234-0.02860.07530.0237-0.0492-0.02810.0006-0.03210.00710.001146.29933.885-55.823
20.3271-0.2498-0.18471.2580.45031.1476-0.0426-0.0254-0.07910.1744-0.01490.25470.0796-0.30040.0575-0.0742-0.05170.04840.03770.01470.061115.99937.606-60.341
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA22 - 24623 - 247
22BB21 - 24922 - 250

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