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- PDB-4fuu: Crystal structure of a leucine aminopeptidase precursor (BT_2548)... -

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Basic information

Entry
Database: PDB / ID: 4fuu
TitleCrystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution
ComponentsLeucine aminopeptidaseLeucyl aminopeptidase
KeywordsHYDROLASE / phosphorylase/hydrolase like fold / peptidase family M28 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Unknown ligand / Leucine aminopeptidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a leucine aminopeptidase precursor (BT_2548) from Bacteroides thetaiotaomicron VPI-5482 at 1.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_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.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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9377
Polymers34,5901
Non-polymers3476
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.236, 41.582, 48.528
Angle α, β, γ (deg.)65.470, 80.430, 78.680
Int Tables number1
Space group name H-MP1
DetailsPACKING ANALYSIS SUGGEST THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Leucine aminopeptidase / Leucyl aminopeptidase


Mass: 34590.254 Da / Num. of mol.: 1 / Fragment: UNP residues 24-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_2548 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A4P9

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Non-polymers , 5 types, 335 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (RESIDUES 24-331) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THIS CONSTRUCT (RESIDUES 24-331) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.00% polyethylene glycol 3350, 0.200M ammonium dihydrogen phosphate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537,0.9796,0.9793
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2011 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97961
30.97931
ReflectionResolution: 1.3→27.993 Å / Num. all: 64313 / Num. obs: 64313 / % possible obs: 93.6 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.234 Å2 / Rsym value: 0.055 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.331.90.4351.9898446380.43591.3
1.33-1.371.90.3551.9877745280.35591.5
1.37-1.411.90.2892.4858444240.28992.1
1.41-1.451.90.233835943260.2392.3
1.45-1.51.90.1853.7811542180.18592.9
1.5-1.551.90.1494.7783940840.14992.8
1.55-1.611.90.1215.7758839520.12193.2
1.61-1.681.90.16.7730938060.193.3
1.68-1.751.90.0897.5698036630.08994
1.75-1.841.90.0768.2664635120.07694.1
1.84-1.941.90.0679.2629733330.06794.3
1.94-2.061.90.0610.2597132080.0694.6
2.06-2.21.80.05611.2546830050.05695.6
2.2-2.371.70.05311.5488728060.05395.7
2.37-2.61.90.04513.4495226040.04595.9
2.6-2.9120.04612.8463823460.04696.7
2.91-3.3620.04812.1418121050.04897.1
3.36-4.1120.03517.2347717630.03597
4.11-5.811.90.02822.6260513390.02895.3
5.81-27.9931.90.03320.412616530.03385.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.5.0110refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.3→27.993 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.485 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.045
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.PHOSPHATE (PO4) FROM THE CRYSTALLIZATION BUFFER AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. THE MODELING OF ZINC IS SUPPORTED BY X-RAY FLUORESCENCE SCANS. THE OCCUPANCY OF THE ZN ATOM WAS REDUCED TO 0.5 FOR ITS REDUCED SCATTERING INDICATED BY ELECTRON DENSITY MAPS. 6. AN UNKNOWN LIGAND (UNL) WAS MODELED AT THE PUTATIVE ACTIVE SITE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1566 3265 5.1 %RANDOM
Rwork0.1181 ---
obs0.12 64273 93.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.53 Å2 / Biso mean: 17.9771 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.14 Å20.01 Å2
2---0.06 Å20.6 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2259 0 22 329 2610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222440
X-RAY DIFFRACTIONr_bond_other_d0.0010.021621
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.9383342
X-RAY DIFFRACTIONr_angle_other_deg0.89833970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.54424.793121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45815388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4351511
X-RAY DIFFRACTIONr_chiral_restr0.0870.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212798
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_mcbond_it2.48531492
X-RAY DIFFRACTIONr_mcbond_other1.2823608
X-RAY DIFFRACTIONr_mcangle_it3.52552412
X-RAY DIFFRACTIONr_scbond_it4.768948
X-RAY DIFFRACTIONr_scangle_it6.6311912
X-RAY DIFFRACTIONr_rigid_bond_restr1.70934061
X-RAY DIFFRACTIONr_sphericity_free12.5215335
X-RAY DIFFRACTIONr_sphericity_bonded5.55153989
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 244 -
Rwork0.208 4377 -
all-4621 -
obs--91.09 %

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