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- PDB-2o1q: CRYSTAL STRUCTURE OF A PUTATIVE ACETYLACETONE DIOXYGENASE (MPE_A3... -

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Database: PDB / ID: 2o1q
TitleCRYSTAL STRUCTURE OF A PUTATIVE ACETYLACETONE DIOXYGENASE (MPE_A3659) FROM METHYLIBIUM PETROLEIPHILUM PM1 AT 1.50 A RESOLUTION
Componentsputative acetyl/propionyl-CoA carboxylase, alpha subunit
KeywordsOXIDOREDUCTASE / PUTATIVE ACETYLACETONE DIOXYGENASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyJelly Rolls / Jelly Rolls / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMethylibium petroleiphilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative acetyl/propionyl-CoA carboxylase, alpha subunit (ZP_00243239.1) from Rubrivivax gelatinosus PM1 (Methylobium petroleophilum PM1) at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.conn_type_id / _struct_conn.id / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS A MIXTURE OF DIMER AND TETRAMER IN SOLUTION. THE PISA SERVER ALSO PREDICTS BOTH THE TETRAMER AND DIMER TO BE STABLE. THE TETRAMER IS DESCRIBED IN REMARK 350.
Remark 999SEQUENCE: (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE: (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. (2) THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE AT THE UNP DATABASE AT THE TIME OF PROCESSING. (3) THE SEQUENCE IS AVAILABLE FROM GENBANK UNDER ACCESSION ID ZP_00243239.1 AND FROM THE UNIPROT ARCHIVE UNDER ACCESSION ID UPI00003CCEF6.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative acetyl/propionyl-CoA carboxylase, alpha subunit
B: putative acetyl/propionyl-CoA carboxylase, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,01615
Polymers31,7122
Non-polymers1,30413
Water3,639202
1
A: putative acetyl/propionyl-CoA carboxylase, alpha subunit
B: putative acetyl/propionyl-CoA carboxylase, alpha subunit
hetero molecules

A: putative acetyl/propionyl-CoA carboxylase, alpha subunit
B: putative acetyl/propionyl-CoA carboxylase, alpha subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,03230
Polymers63,4254
Non-polymers2,60826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area16580 Å2
ΔGint-308 kcal/mol
Surface area21630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.020, 62.020, 133.800
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS A MIXTURE OF DIMER AND TETRAMER IN SOLUTION. THE PISA SERVER ALSO PREDICTS BOTH THE TETRAMER AND DIMER TO BE STABLE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein putative acetyl/propionyl-CoA carboxylase, alpha subunit


Mass: 15856.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylibium petroleiphilum (bacteria) / Strain: PM1
Description: Methylobium petroleophilum is another scientific name of the source organism
Gene: ZP_00243239.1 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 215 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.03 Å3/Da / Density % sol: 39.33 %
Description: DATA FROM TWO CRYSTALS WERE USED FOR THE STRUCTURE DETERMINATION. ONE CRYSTAL WAS USED FOR MAD PHASING EXPERIMENTS AND TRACING AT A RESOLUTION OF 2.0 ANGTROMS. THE 2.0 ANGSTROM MODEL WAS ...Description: DATA FROM TWO CRYSTALS WERE USED FOR THE STRUCTURE DETERMINATION. ONE CRYSTAL WAS USED FOR MAD PHASING EXPERIMENTS AND TRACING AT A RESOLUTION OF 2.0 ANGTROMS. THE 2.0 ANGSTROM MODEL WAS REFINED TO AN ENHANCED RESOLUTION OF 1.50 ANGSTROMS USING DATA FROM A SEPARATE CRYSTAL WITH THE 2 ANGSTROM MAD PHASES FROM THE FIRST CRYSTAL USED AS PHASE RESTRAINTS.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 20.0% PEG-1000, 0.2M Zn(OAc)2, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL1-511.000017
SYNCHROTRONAPS 23-ID-D20.97942, 0.97921, 0.94645
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 11, 20061m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
MARMOSAIC 300 mm CCD2CCDOct 20, 2006Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) Double Crystal MonochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000171
20.979421
30.979211
40.946451
ReflectionResolution: 1.5→29.437 Å / Num. obs: 42659 / % possible obs: 99.7 % / Biso Wilson estimate: 16.91 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 9.49
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.5-1.550.7321.9251451,297.7
1.55-1.620.6392.3326701,2100
1.62-1.690.5662.7277861,2100
1.69-1.780.4393.4292881,2100
1.78-1.890.3134.4279331,299.9
1.89-2.040.2185.9280911,299.8
2.04-2.240.2079.2520791,299.9
2.24-2.560.14212.4546781,299.9
2.56-3.230.08319556551,299.8
3.23-29.40.05733.6579931,299.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→29.437 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.939 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). A ZN ATOM ON EACH OF THE TWO SUBUNITS IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAIN OF HIS 59, HIS 101, AND ACETATE. A ZINC ATOM ON SUBUNIT B IS COORDINATED TO THE SIDE CHAINS OF GLU 136, ASP 137 AND FOUR WATER MOLECULES. ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT OF THE ZINC IONS. (5). UNEXPLAINED ELECTRON DENSITIES OBSERVED NEAR RESIDUE 111 ON THE A SUBUNIT AND RESIDUES 141-143 ON THE B SUBUNIT WERE NOT MODELED. (6). FOUR MOLECULES OF POLYETHYLENE GLYCOL 200 (PG4) USED AS A CRYOPROTECTANT, FIVE ACETATE (ACT) AND ONE CL ION FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2177 5.1 %RANDOM
Rwork0.181 ---
obs0.183 42575 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 58 202 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222373
X-RAY DIFFRACTIONr_bond_other_d0.0010.021577
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9493219
X-RAY DIFFRACTIONr_angle_other_deg0.93533843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39523.84691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42915324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.698155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022724
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined0.2330.2498
X-RAY DIFFRACTIONr_nbd_other0.2020.21517
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21142
X-RAY DIFFRACTIONr_nbtor_other0.0910.21260
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2171
X-RAY DIFFRACTIONr_metal_ion_refined0.2150.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.230
X-RAY DIFFRACTIONr_mcbond_it2.19431549
X-RAY DIFFRACTIONr_mcbond_other0.6283606
X-RAY DIFFRACTIONr_mcangle_it2.78452382
X-RAY DIFFRACTIONr_scbond_it4.3118997
X-RAY DIFFRACTIONr_scangle_it5.22111837
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 174 -
Rwork0.227 2892 -
obs-3066 98.36 %
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)
10.75040.1842-0.13710.67490.08020.53510.0434-0.1075-0.03820.0526-0.02740.02170.03370.0314-0.0161-0.04940.0044-0.0008-0.02910.0216-0.032122.343219.436710.2985
20.77830.23910.08650.6590.10840.78510.0641-0.14770.03890.0210.0062-0.0406-0.0990.1137-0.0703-0.0305-0.01030.01230.0069-0.0421-0.024140.662340.67510.6169
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 144 / Label seq-ID: 2 - 145

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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