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- PDB-4mtu: beta-Alanyl-CoA:Ammonia Lyase from Clostridium propionicum -

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Basic information

Entry
Database: PDB / ID: 4mtu
Titlebeta-Alanyl-CoA:Ammonia Lyase from Clostridium propionicum
ComponentsBeta-alanyl-CoA:ammonia lyase 2
KeywordsLYASE / hot dog fold
Function / homologyHotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / lyase activity / Roll / metal ion binding / Alpha Beta / Beta-alanyl-CoA:ammonia lyase 2
Function and homology information
Biological speciesClostridium propionicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.97 Å
AuthorsHeine, A. / Reuter, K.
CitationJournal: Proteins / Year: 2014
Title: High resolution crystal structure of Clostridium propionicum beta-alanyl-CoA:ammonia lyase, a new member of the "hot dog fold" protein superfamily.
Authors: Heine, A. / Herrmann, G. / Selmer, T. / Terwesten, F. / Buckel, W. / Reuter, K.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 3, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: 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_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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-alanyl-CoA:ammonia lyase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1863
Polymers16,0241
Non-polymers1612
Water2,666148
1
A: Beta-alanyl-CoA:ammonia lyase 2
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)97,11418
Polymers96,1456
Non-polymers96912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area18240 Å2
ΔGint-386 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.110, 78.110, 102.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-350-

HOH

21A-415-

HOH

31A-431-

HOH

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Components

#1: Protein Beta-alanyl-CoA:ammonia lyase 2


Mass: 16024.199 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Clostridium propionicum (bacteria) / References: UniProt: Q6KC22
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% PEG MME 550, 100 mmol L-1 MES, 50 mmol L-1 ZnSO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.90, 1.28257, 1.28314
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 24, 2003 / Details: Silicon, active surface 50 nm Rh-coated mirrors
RadiationMonochromator: Si-111 double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.282571
31.283141
ReflectionResolution: 0.97→20 Å / Num. all: 107732 / Num. obs: 107732 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rsym value: 0.066 / Net I/σ(I): 35.3
Reflection shellResolution: 0.97→0.99 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 5120 / Rsym value: 0.515 / % possible all: 95.5

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Processing

Software
NameClassification
MAR345dtbdata collection
SHELXDphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 0.97→20 Å / Num. parameters: 11817 / Num. restraintsaints: 24192 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.159 5388 5 %RANDOM
Rwork0.1456 ---
all0.1459 107706 --
obs0.1459 102318 98.8 %-
Refine analyzeNum. disordered residues: 18 / Occupancy sum non hydrogen: 1243
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 6 148 1247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0167
X-RAY DIFFRACTIONs_angle_d0.0324
X-RAY DIFFRACTIONs_from_restr_planes0.4008
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1146
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.0105
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.03
X-RAY DIFFRACTIONs_approx_iso_adps0.1304

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