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- PDB-2p7h: Crystal structure of a sam dependent methyl-transferase type 12 f... -

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Entry
Database: PDB / ID: 2p7h
TitleCrystal structure of a sam dependent methyl-transferase type 12 family protein (eca1738) from pectobacterium atrosepticum scri1043 at 1.85 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 / SAD / Resolution: 1.85 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 1.85 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 / 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.conn_type_id / _struct_conn.id / _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
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER 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.

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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
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,88922
Polymers114,7434
Non-polymers1,14618
Water12,196677
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13050 Å2
ΔGint-39 kcal/mol
Surface area34550 Å2
MethodPISA
2
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)463,55688
Polymers458,97116
Non-polymers4,58572
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area62910 Å2
ΔGint-203 kcal/mol
Surface area127500 Å2
MethodPISA
3
B: Hypothetical protein
D: Hypothetical protein
hetero molecules

B: Hypothetical protein
D: Hypothetical protein
hetero molecules

A: Hypothetical protein
C: Hypothetical protein
hetero molecules

A: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,77844
Polymers229,4868
Non-polymers2,29336
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area19520 Å2
ΔGint-86 kcal/mol
Surface area75680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.949, 117.949, 150.532
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11B-251-

CL

21D-250-

CL

31B-333-

HOH

41D-341-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLNGLNAA22 - 24923 - 250
2GLYGLYBB22 - 24623 - 247
3GLNGLNCC22 - 24923 - 250
4GLYGLYDD22 - 24623 - 247

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Hypothetical protein


Mass: 28685.703 Da / Num. of mol.: 4
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, 695 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.28 Å3/Da / Density % sol: 46.07 %
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 Å
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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.85→29.934 Å / Num. obs: 90790 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.17 Å2 / Rmerge(I) obs: 0.146 / Rsym value: 0.146 / Net I/σ(I): 4.1
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
1.85-1.97.40.74903766341.059100
1.9-1.957.40.94768564610.831100
1.95-2.017.41.24650462900.655100
2.01-2.077.41.44524561050.522100
2.07-2.147.41.84409159440.427100
2.14-2.217.42.24258557400.338100
2.21-2.297.42.34104955480.3100
2.29-2.397.433979853650.253100
2.39-2.497.43.43805251250.221100
2.49-2.627.443665049420.185100
2.62-2.767.44.53460946620.163100
2.76-2.937.45.13296944510.137100
2.93-3.137.45.53105942050.119100
3.13-3.387.45.72887539150.108100
3.38-3.77.37.32652236150.083100
3.7-4.147.37.92397732790.07799.9
4.14-4.787.37.82127629240.07899.8
4.78-5.857.28.41794724960.06999.7
5.85-8.2779.31381219620.06399.6
8.27-29.936.510.1731311270.05396.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.934 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.633 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106
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 EDO ARE MODELED BASED ON CRYSTALLIZATION OR CRYO CONDITIONS. 5. THE N-TERMINAL RESIDUES 0-20 IN CHAINS A,B,C,D ARE DISORDERED. 6. RAMACHANDRAN OUTLIERS FOR RESIDUE 199 ARE SUPPORTED BY UNAMBIGUOUS ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4551 5 %RANDOM
Rwork0.149 ---
all0.15 ---
obs0.15 90758 99.85 %-
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: 22.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7263 0 67 677 8007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227676
X-RAY DIFFRACTIONr_bond_other_d0.0010.025206
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.94110438
X-RAY DIFFRACTIONr_angle_other_deg0.906312603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8085974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.79123.564404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.637151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0111560
X-RAY DIFFRACTIONr_chiral_restr0.0890.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028728
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021708
X-RAY DIFFRACTIONr_nbd_refined0.2180.21433
X-RAY DIFFRACTIONr_nbd_other0.1950.25579
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23692
X-RAY DIFFRACTIONr_nbtor_other0.0850.24111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2541
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0670.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3350.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1190.22
X-RAY DIFFRACTIONr_mcbond_it1.71434636
X-RAY DIFFRACTIONr_mcbond_other0.69231877
X-RAY DIFFRACTIONr_mcangle_it2.80257484
X-RAY DIFFRACTIONr_scbond_it4.56883105
X-RAY DIFFRACTIONr_scangle_it6.836112920
Refine LS restraints NCS

Ens-ID: 1 / Number: 2992 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.280.5
2BMEDIUM POSITIONAL0.270.5
3CMEDIUM POSITIONAL0.290.5
4DMEDIUM POSITIONAL0.270.5
1AMEDIUM THERMAL1.012
2BMEDIUM THERMAL0.992
3CMEDIUM THERMAL1.012
4DMEDIUM THERMAL1.012
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 344 -
Rwork0.209 6290 -
obs-6634 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)
11.13950.2724-0.47710.3745-0.03631.0436-0.0071-0.1548-0.18190.0398-0.0436-0.04640.15670.05550.0507-0.01670.0137-0.0047-0.04830.03730.041223.90315.13152.47
20.33530.35150.13970.41910.13530.83380.0443-0.04460.03940.0356-0.07130.0541-0.0388-0.08570.0271-0.02620.00930.0017-0.0386-0.0025-0.008726.5945.75456.739
30.40140.1991-0.09910.9248-0.31991.0745-0.030.0303-0.04-0.11150.0018-0.13730.01850.16130.0281-0.0660.010.0345-0.0136-0.00290.029744.96237.29522.873
40.51470.37690.1310.38280.14550.8004-0.07310.04960.0474-0.05320.04510.0371-0.0756-0.03620.028-0.04340.0051-0.0013-0.0142-0.0008-0.010114.47133.32618.765
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA21 - 24922 - 250
22BB21 - 24622 - 247
33CC21 - 24922 - 250
44DD21 - 24622 - 247

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