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- PDB-4ne7: Crystal Structure of engineered Kumamolisin-As from Alicyclobacil... -

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Basic information

Entry
Database: PDB / ID: 4ne7
TitleCrystal Structure of engineered Kumamolisin-As from Alicyclobacillus sendaiensis, Northeast Structural Genomics Consortium (NESG) Target OR367
ComponentsKumamolisin-As
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ENGINEERED PROTEIN
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase S53, activation domain / Sedolisin domain / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold ...Peptidase S53, activation domain / Sedolisin domain / Pro-kumamolisin, activation domain / Sedolisin domain profile. / Pro-kumamolisin, activation domain / Peptidase S8/S53 domain / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAlicyclobacillus sendaiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsGuan, R. / Pultz, I.S. / Siegel, J.B. / Seetharaman, J. / Kornhaber, G. / Maglaqui, M. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. ...Guan, R. / Pultz, I.S. / Siegel, J.B. / Seetharaman, J. / Kornhaber, G. / Maglaqui, M. / Mao, L. / Xiao, R. / Everett, J.K. / Baker, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target OR367
Authors: Guan, R. / Pultz, I.S. / Seetharaman, J. / Kornhaber, G. / Mao, L. / Xiao, R. / Maglaqui, M. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T.
History
DepositionOct 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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: Kumamolisin-As
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3966
Polymers39,0691
Non-polymers3275
Water2,450136
1
A: Kumamolisin-As
hetero molecules

A: Kumamolisin-As
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,79212
Polymers78,1382
Non-polymers65410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+2/31
Buried area2610 Å2
ΔGint-325 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.885, 110.885, 75.992
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-565-

HOH

Detailsmonomer,37.57 kD,90.1%

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Components

#1: Protein Kumamolisin-As


Mass: 39068.934 Da / Num. of mol.: 1 / Fragment: UNP residues 190-553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus sendaiensis (bacteria)
Gene: scpA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GB88*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Protein solution - 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution - 15% PEG 8000, 0.1 M MES pH 6.0, 0.2 M Zinc Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.5→44.8 Å / Num. all: 19077 / Num. obs: 19077 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.2 % / Biso Wilson estimate: 34.05 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 24.83
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 9.29 / Num. unique all: 1882 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SN7

1sn7


Resolution: 2.497→44.789 Å / Occupancy max: 1 / Occupancy min: 0.56 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.72 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1783 9.91 %RANDOM
Rwork0.198 ---
all0.202 19077 --
obs0.202 17999 94.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.48 Å2 / Biso mean: 35.053 Å2 / Biso min: 4.62 Å2
Refinement stepCycle: LAST / Resolution: 2.497→44.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 0 5 136 2682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032606
X-RAY DIFFRACTIONf_angle_d0.7873579
X-RAY DIFFRACTIONf_chiral_restr0.047402
X-RAY DIFFRACTIONf_plane_restr0.004485
X-RAY DIFFRACTIONf_dihedral_angle_d11.453896
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.497-2.5650.311290.2381206133593
2.565-2.640.3221130.2431036114978
2.64-2.7250.4381160.3311045116180
2.725-2.8230.3161360.2291217135394
2.823-2.9360.2851390.2081261140097
2.936-3.0690.2971410.2121274141598
3.069-3.2310.2511450.2021307145299
3.231-3.4330.2551350.2161273140897
3.433-3.6980.2511410.2261256139795
3.698-4.070.2581400.1911264140496
4.07-4.6590.1671460.13813271473100
4.659-5.8670.1791480.15513561504100
5.867-44.7960.1871540.18613941548100

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