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- PDB-5l9w: Crystal structure of the Apc core complex -

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Basic information

Entry
Database: PDB / ID: 5l9w
TitleCrystal structure of the Apc core complex
Components(Acetophenone carboxylase ...) x 4
KeywordsLIGASE / Acetophenone carboxylase
Function / homology
Function and homology information


acetophenone carboxylase / 5-oxoprolinase (ATP-hydrolyzing) activity / ligase activity / glutathione metabolic process / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / : / : / : / Acetophenone carboxylase beta subunit/Acetone carboxylase gamma subunit / Acetone carboxylase gamma subunit / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase, N-terminal / Oxoprolinase family / : ...: / : / : / : / Acetophenone carboxylase beta subunit/Acetone carboxylase gamma subunit / Acetone carboxylase gamma subunit / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase, N-terminal / Oxoprolinase family / : / Hydantoinase B/oxoprolinase / Hydantoinase/oxoprolinase N-terminal region / Hydantoinase/oxoprolinase C-terminal domain / Hydantoinase A/oxoprolinase / Hydantoinase/oxoprolinase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / : / Acetophenone carboxylase alpha subunit / Acetophenone carboxylase beta subunit / Acetophenone carboxylase gamma subunit / Acetophenone carboxylase delta subunit
Similarity search - Component
Biological speciesAromatoleum aromaticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsWarkentin, E. / Weidenweber, S. / Ermler, U.
Citation
Journal: Sci Rep / Year: 2017
Title: Structure of the acetophenone carboxylase core complex: prototype of a new class of ATP-dependent carboxylases/hydrolases.
Authors: Weidenweber, S. / Schuhle, K. / Demmer, U. / Warkentin, E. / Ermler, U. / Heider, J.
#1: Journal: To Be Published
Title: A new secondary structure in proteins: The G column, a bundle of glycine-rich type II polyproline helices
Authors: Warkentin, E. / Weidenweber, S. / Schuehle, K. / Demmer, U. / Heider, J. / Ermler, U.
History
DepositionJun 11, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetophenone carboxylase delta subunit
B: Acetophenone carboxylase gamma subunit
b: Acetophenone carboxylase alpha subunit
C: Acetophenone carboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,85013
Polymers240,8674
Non-polymers1,9849
Water25214
1
A: Acetophenone carboxylase delta subunit
C: Acetophenone carboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3797
Polymers90,5002
Non-polymers8795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetophenone carboxylase gamma subunit
b: Acetophenone carboxylase alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,4716
Polymers150,3672
Non-polymers1,1044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)240.080, 240.080, 336.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Acetophenone carboxylase ... , 4 types, 4 molecules ABbC

#1: Protein Acetophenone carboxylase delta subunit / Acetophenone carboxylase 75 kDa subunit


Mass: 75484.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / References: UniProt: Q5P5G5, acetophenone carboxylase
#2: Protein Acetophenone carboxylase gamma subunit / Acetophenone carboxylase 87 kDa subunit


Mass: 80431.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / References: UniProt: Q5P5G4, acetophenone carboxylase
#3: Protein Acetophenone carboxylase alpha subunit / Acetophenone carboxylase 70 kDa subunit


Mass: 69935.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / References: UniProt: Q5P5G2, acetophenone carboxylase
#4: Protein Acetophenone carboxylase beta subunit / Acetophenone carboxylase 15 kDa subunit


Mass: 15015.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / References: UniProt: Q5P5G3, acetophenone carboxylase

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Non-polymers , 5 types, 23 molecules

#5: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#6: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 5.81 Å3/Da / Density % sol: 78.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 34 - 50 % (v/v) PEE, 0.1 M Hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 121963 / % possible obs: 96.4 % / Redundancy: 14 % / Rrim(I) all: 0.117 / Net I/σ(I): 25
Reflection shellResolution: 2.9→3.1 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 1.7 / Rrim(I) all: 2.42 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
BUCCANEERmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.9→19.971 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.62
RfactorNum. reflection% reflection
Rfree0.2351 6087 5.02 %
Rwork0.1965 --
obs0.1985 121173 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→19.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16670 0 77 14 16761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00917115
X-RAY DIFFRACTIONf_angle_d1.10923213
X-RAY DIFFRACTIONf_dihedral_angle_d14.97610257
X-RAY DIFFRACTIONf_chiral_restr0.0562583
X-RAY DIFFRACTIONf_plane_restr0.0073031
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.93290.44611950.45683576X-RAY DIFFRACTION91
2.9329-2.96730.44971890.45573584X-RAY DIFFRACTION91
2.9673-3.00330.46661870.45013580X-RAY DIFFRACTION91
3.0033-3.04120.46471860.4333594X-RAY DIFFRACTION91
3.0412-3.08110.44032060.39983603X-RAY DIFFRACTION92
3.0811-3.12310.39031830.39153622X-RAY DIFFRACTION92
3.1231-3.16760.40571950.35793678X-RAY DIFFRACTION93
3.1676-3.21470.38191850.35693634X-RAY DIFFRACTION93
3.2147-3.26470.38151830.35423710X-RAY DIFFRACTION94
3.2647-3.3180.36881850.3333753X-RAY DIFFRACTION95
3.318-3.37490.36352300.3073740X-RAY DIFFRACTION95
3.3749-3.4360.32132190.28583773X-RAY DIFFRACTION96
3.436-3.50170.30581950.25883781X-RAY DIFFRACTION96
3.5017-3.57280.28332020.23593823X-RAY DIFFRACTION96
3.5728-3.65010.24332300.20763809X-RAY DIFFRACTION97
3.6501-3.73440.22941920.20433858X-RAY DIFFRACTION98
3.7344-3.82720.23982220.18933872X-RAY DIFFRACTION98
3.8272-3.92990.22131740.17973934X-RAY DIFFRACTION98
3.9299-4.04460.22781810.16553909X-RAY DIFFRACTION98
4.0446-4.1740.18581920.15583919X-RAY DIFFRACTION98
4.174-4.32180.17752280.14543917X-RAY DIFFRACTION99
4.3218-4.49290.17342090.13543962X-RAY DIFFRACTION99
4.4929-4.69490.16981980.13443975X-RAY DIFFRACTION99
4.6949-4.93890.17282070.13583959X-RAY DIFFRACTION99
4.9389-5.2430.1982320.15133977X-RAY DIFFRACTION99
5.243-5.63940.20472060.16364013X-RAY DIFFRACTION100
5.6394-6.19150.24272200.19254029X-RAY DIFFRACTION100
6.1915-7.05270.24782040.18694101X-RAY DIFFRACTION100
7.0527-8.75910.2032160.16394113X-RAY DIFFRACTION100
8.7591-19.97190.18542360.15974288X-RAY DIFFRACTION100
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)
10.97670.05980.06781.1521-0.29411.7004-0.013-0.13280.27460.0935-0.05030.1402-0.4175-0.08420.07130.60870.0519-0.02250.4123-0.04750.5003199.098347.435419.3465
21.3398-0.2372-0.34112.78920.55861.14550.00750.03590.50730.0618-0.0110.4717-1.0211-0.6752-0.01381.23610.3017-0.03860.7628-0.13481.008185.809174.701918.2585
32.86561.14520.75812.48510.32631.81930.0265-0.27650.39290.3621-0.02960.2389-1.0596-0.02520.04031.63690.16330.04650.6829-0.17210.9464197.695277.759426.6631
40.6287-0.8283-0.30022.73110.15740.78260.21930.25650.3116-0.814-0.0944-0.262-0.1222-0.1297-0.12421.34250.2772-0.12570.93960.18780.9883193.194181.5599-44.0939
50.80780.25810.18960.7123-0.22191.0344-0.00320.1930.1608-0.2431-0.0718-0.0222-0.21220.23920.08150.80180.0962-0.01650.57240.03970.5311216.727745.9605-11.8843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 579 )
2X-RAY DIFFRACTION2chain 'A' and (resid 580 through 684 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 125 )
4X-RAY DIFFRACTION4chain 'b' and (resid 1 through 654 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 718 )

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