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- PDB-3nz2: Crystal Structure of Hexapeptide-Repeat containing-Acetyltransfer... -

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Basic information

Entry
Database: PDB / ID: 3nz2
TitleCrystal Structure of Hexapeptide-Repeat containing-Acetyltransferase VCA0836 Complexed with Acetyl Co Enzyme A from Vibrio cholerae O1 biovar eltor
ComponentsHexapeptide-repeat containing-acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / beta-helix / methyltransferase
Function / homology
Function and homology information


O-acyltransferase activity / acetyltransferase activity / metal ion binding / cytosol
Similarity search - Function
Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...Maltose/galactoside acetyltransferase / Maltose acetyltransferase / Maltose acetyltransferase / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETIC ACID / 1,4-BUTANEDIOL / Hexapeptide-repeat containing-acetyltransferase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKim, Y. / Maltseva, N. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Hexapeptide-Repeat containing-Acetyltransferase VCA0836 Complexed with Acetyl Co Enzyme A from Vibrio cholerae O1 biovar eltor
Authors: Kim, Y. / Maltseva, N. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexapeptide-repeat containing-acetyltransferase
B: Hexapeptide-repeat containing-acetyltransferase
C: Hexapeptide-repeat containing-acetyltransferase
D: Hexapeptide-repeat containing-acetyltransferase
E: Hexapeptide-repeat containing-acetyltransferase
F: Hexapeptide-repeat containing-acetyltransferase
G: Hexapeptide-repeat containing-acetyltransferase
H: Hexapeptide-repeat containing-acetyltransferase
I: Hexapeptide-repeat containing-acetyltransferase
J: Hexapeptide-repeat containing-acetyltransferase
K: Hexapeptide-repeat containing-acetyltransferase
L: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,76345
Polymers260,75712
Non-polymers11,00633
Water18,4111022
1
A: Hexapeptide-repeat containing-acetyltransferase
B: Hexapeptide-repeat containing-acetyltransferase
C: Hexapeptide-repeat containing-acetyltransferase
D: Hexapeptide-repeat containing-acetyltransferase
E: Hexapeptide-repeat containing-acetyltransferase
F: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,94324
Polymers130,3796
Non-polymers5,56518
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Hexapeptide-repeat containing-acetyltransferase
H: Hexapeptide-repeat containing-acetyltransferase
I: Hexapeptide-repeat containing-acetyltransferase
J: Hexapeptide-repeat containing-acetyltransferase
K: Hexapeptide-repeat containing-acetyltransferase
L: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,81921
Polymers130,3796
Non-polymers5,44115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Hexapeptide-repeat containing-acetyltransferase
B: Hexapeptide-repeat containing-acetyltransferase
C: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,98513
Polymers65,1893
Non-polymers2,79610
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-85 kcal/mol
Surface area24650 Å2
MethodPISA
4
D: Hexapeptide-repeat containing-acetyltransferase
E: Hexapeptide-repeat containing-acetyltransferase
F: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95811
Polymers65,1893
Non-polymers2,7688
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-54 kcal/mol
Surface area24680 Å2
MethodPISA
5
G: Hexapeptide-repeat containing-acetyltransferase
H: Hexapeptide-repeat containing-acetyltransferase
I: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,86410
Polymers65,1893
Non-polymers2,6747
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-64 kcal/mol
Surface area24650 Å2
MethodPISA
6
J: Hexapeptide-repeat containing-acetyltransferase
K: Hexapeptide-repeat containing-acetyltransferase
L: Hexapeptide-repeat containing-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,95611
Polymers65,1893
Non-polymers2,7668
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-58 kcal/mol
Surface area25160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.316, 135.801, 120.535
Angle α, β, γ (deg.)90.00, 91.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Hexapeptide-repeat containing-acetyltransferase


Mass: 21729.754 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Strain: N16961 / Gene: VC_A0836 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q9KLB0

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Non-polymers , 7 types, 1055 molecules

#2: Chemical
ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-BU1 / 1,4-BUTANEDIOL / 1,4-Butanediol


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Acetate pH 4.5, 20% (v/v) 1,4-butanediol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2009 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 100668 / Num. obs: 100668 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.8 % / Rsym value: 0.177 / Net I/σ(I): 4.6
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.778 / % possible all: 99.2

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3ECT
Resolution: 2.35→46.632 Å / SU ML: 0.36 / Isotropic thermal model: mixed / σ(F): 1.34 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 5018 5.01 %
Rwork0.188 --
obs0.1912 100184 96.89 %
all-100184 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.869 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.0717 Å2-0 Å2-1.0181 Å2
2---1.8922 Å20 Å2
3---10.9638 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17020 0 690 1022 18732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318136
X-RAY DIFFRACTIONf_angle_d1.44324634
X-RAY DIFFRACTIONf_dihedral_angle_d23.7957217
X-RAY DIFFRACTIONf_chiral_restr0.0962722
X-RAY DIFFRACTIONf_plane_restr0.0113151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.4340.32324920.24149232X-RAY DIFFRACTION94
2.434-2.53140.30695030.22679567X-RAY DIFFRACTION98
2.5314-2.64660.29054870.22299616X-RAY DIFFRACTION98
2.6466-2.78610.29315030.19959551X-RAY DIFFRACTION98
2.7861-2.96070.26645180.18029469X-RAY DIFFRACTION97
2.9607-3.18920.24615030.17489398X-RAY DIFFRACTION96
3.1892-3.51010.24625080.17369313X-RAY DIFFRACTION95
3.5101-4.01770.22874730.16969444X-RAY DIFFRACTION96
4.0177-5.06090.20645070.15369673X-RAY DIFFRACTION98
5.0609-46.64160.25565240.21849903X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1548-0.0774-0.00670.0682-0.0350.0544-0.02580.0292-0.0534-0.04110.02360.03520.02190.0624-0.00620.0852-0.0149-0.01120.1044-0.0130.02485.6749-1.702547.9313
20.1883-0.03840.03550.55860.07410.57440.06170.0456-0.01880.118-0.02270.1760.04560.0064-0.00380.042-0.00930.02960.0282-0.01160.0578-8.615915.153960.0164
30.149-0.10980.08950.19660.03310.2532-0.06440.0482-0.06420.07210.05690.0502-0.05190.0233-0.01620.07580.01030.02580.0407-0.01220.02915.4174-2.230972.8382
40.24830.10560.09820.20840.01850.3551-0.09470.14150.1294-0.03660.02010.0593-0.03480.00650.06720.0453-0.0044-0.03750.11030.02310.091732.235937.495545.7251
50.69330.02910.17450.1940.15840.23940.00360.0799-0.1162-0.0002-0.0586-0.0005-0.00380.04350.03460.0411-0.0089-0.00450.040.00580.074444.229421.639260.1577
60.860.2804-0.02950.2460.21450.4065-0.0405-0.14140.34320.0283-0.05720.16830.0051-0.01660.08620.03440.0035-0.00990.0562-0.06460.162431.007239.873470.2416
70.255-0.10160.10180.6159-0.14320.2848-0.02540.1678-0.0433-0.04150.00180.10330.01780.05710.02140.02120.0034-0.00860.0755-0.00320.183842.727952.2446108.2846
81.115-0.02990.15060.2276-0.10570.0750.01120.0631-0.2702-0.00010.01540.0166-0.01080.0028-0.0270.00290.0132-0.00480.01690.05590.153941.681252.648132.3963
90.36140.08450.10890.23490.12360.34480.01540.05610.09860.0165-0.07030.18890.05670.01970.04960.0376-0.0022-0.03010.05190.01060.171228.190768.8259121.0684
100.33650.09870.12610.5512-0.12840.10640.01210.01080.01950.0677-0.02970.0868-0.03680.03310.0090.03220.00720.00820.0357-0.00930.019668.252793.2018130.5801
110.25720.0776-0.02540.2148-0.03740.0138-0.03440.11540.01630.03080.06890.042-0.0422-0.0367-0.03350.04520.0092-0.00870.09150.02950.023868.512491.5426106.4601
120.28180.15010.04840.2011-0.10920.17010.09140.0092-0.0530.0832-0.052-0.0361-0.0471-0.0441-0.02370.0472-0.0048-0.00570.0814-0.00020.022580.726476.3433119.5867
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9chain I
10X-RAY DIFFRACTION10chain J
11X-RAY DIFFRACTION11chain K
12X-RAY DIFFRACTION12chain L

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