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- PDB-3c6c: Crystal structure of a putative 3-keto-5-aminohexanoate cleavage ... -

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Basic information

Entry
Database: PDB / ID: 3c6c
TitleCrystal structure of a putative 3-keto-5-aminohexanoate cleavage enzyme (reut_c6226) from ralstonia eutropha jmp134 at 1.72 A resolution
Components3-keto-5-aminohexanoate cleavage enzyme
KeywordsHYDROLASE / Duf849 family protein / tim beta/alpha-barrel fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


3-keto-5-aminohexanoate cleavage activity
Similarity search - Function
3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / 3-keto-5-aminohexanoate cleavage enzyme
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 3-keto-5-aminohexanoate cleavage enzyme (YP_293392.1) from Ralstonia eutropha JMP134 at 1.72 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_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_type.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 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-keto-5-aminohexanoate cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2647
Polymers34,8541
Non-polymers4106
Water7,044391
1
A: 3-keto-5-aminohexanoate cleavage enzyme
hetero molecules

A: 3-keto-5-aminohexanoate cleavage enzyme
hetero molecules

A: 3-keto-5-aminohexanoate cleavage enzyme
hetero molecules

A: 3-keto-5-aminohexanoate cleavage enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,05728
Polymers139,4174
Non-polymers1,64024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.339, 121.397, 133.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-keto-5-aminohexanoate cleavage enzyme


Mass: 34854.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Species: Cupriavidus necator / Strain: JMP134 / Gene: YP_293392.1, Reut_C6226 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46MU0

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Non-polymers , 5 types, 397 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: NANODROP, 0.2M Lithium acetate, 20.0% PEG 3350, No Buffer pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97964 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 1.72→38.72 Å / Num. obs: 43691 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.155 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.66
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.72-1.790.4442.7170844860199.9
1.79-1.870.3513.41737147511100
1.87-1.970.2514.9173264801199.6
1.97-2.090.1666.9169914690199.3
2.09-2.250.1469.4195554782199.8
2.25-2.480.16111.7267824936199.9
2.48-2.840.12915.63436948891100
2.84-3.570.07223505348711100
3.57-38.720.05227.1348245112199.6

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→38.72 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.669 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.082
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. AN X-RAY EMISSION SPECTRUM AND AN X-RAY FLUORESCENCE SCAN NEAR NI ABSORPTION EDGE TAKEN FROM THE SAMPLE VERIFY THE PRESENCE OF NI METAL. THE OCCUPANCY WAS ADJUSTED TO REFLECT THE DENSITY AND TO PROVIDE A SIMILAR B-FACTOR AS THE COORDINATING PROTEIN ATOMS. 5. EDO, ACT AND PEG FROM THE CRYSTALLIZATION BUFFER WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.184 2196 5 %RANDOM
Rwork0.153 ---
obs0.154 43691 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.493 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.3 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.72→38.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 24 391 2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222316
X-RAY DIFFRACTIONr_bond_other_d0.0010.021569
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.9843154
X-RAY DIFFRACTIONr_angle_other_deg1.63433849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87524.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53715382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4881517
X-RAY DIFFRACTIONr_chiral_restr0.0830.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212602
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02437
X-RAY DIFFRACTIONr_mcbond_it1.52731492
X-RAY DIFFRACTIONr_mcbond_other0.4443603
X-RAY DIFFRACTIONr_mcangle_it2.352412
X-RAY DIFFRACTIONr_scbond_it3.748824
X-RAY DIFFRACTIONr_scangle_it5.44511733
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 163 -
Rwork0.235 3051 -
all-3214 -
obs--99.78 %
Refinement TLS params.Method: refined / Origin x: 31.9292 Å / Origin y: 39.8619 Å / Origin z: 49.9412 Å
111213212223313233
T-0.0298 Å20.016 Å2-0.0291 Å2--0.0315 Å2-0.0176 Å2---0.0195 Å2
L0.1893 °2-0.0274 °2-0.2387 °2-0.6633 °20.1958 °2--0.9667 °2
S-0.0236 Å °0.0158 Å °-0.0156 Å °0.1012 Å °0.0247 Å °-0.092 Å °0.1132 Å °0.0396 Å °-0.0011 Å °

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