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- PDB-4fgm: Crystal structure of the aminopeptidase N family protein Q5QTY1 f... -

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Basic information

Entry
Database: PDB / ID: 4fgm
TitleCrystal structure of the aminopeptidase N family protein Q5QTY1 from Idiomarina loihiensis. Northeast Structural Genomics Consortium Target IlR60.
ComponentsAminopeptidase N family protein
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / peptidase_M61 / PDZ / PDZ_2
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Immunoglobulin-like - #3650 / Peptidase M61, catalytic domain / Peptidase M61 / Peptidase M61, N-terminal domain / M61 glycyl aminopeptidase / Peptidase M61 N-terminal domain / PDZ domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / PDZ domain ...Immunoglobulin-like - #3650 / Peptidase M61, catalytic domain / Peptidase M61 / Peptidase M61, N-terminal domain / M61 glycyl aminopeptidase / Peptidase M61 N-terminal domain / PDZ domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / PDZ domain / Pdz3 Domain / Peptidase M4/M1, CTD superfamily / PDZ superfamily / Roll / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
MALEIC ACID / Aminopeptidase N family protein, contains PDZ domain
Similarity search - Component
Biological speciesIdiomarina loihiensis L2TR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.394 Å
AuthorsVorobiev, S. / Su, M. / Tong, T. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the aminopeptidase N family protein Q5QTY1 from Idiomarina loihiensis.
Authors: Vorobiev, S. / Su, M. / Tong, T. / Kohan, E. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_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_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: Aminopeptidase N family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7073
Polymers68,5261
Non-polymers1812
Water3,999222
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aminopeptidase N family protein
hetero molecules

A: Aminopeptidase N family protein
hetero molecules

A: Aminopeptidase N family protein
hetero molecules

A: Aminopeptidase N family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,82912
Polymers274,1034
Non-polymers7268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area16320 Å2
ΔGint-160 kcal/mol
Surface area81470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.657, 119.657, 220.134
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Detailsmonomer according to aggregation screening

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Components

#1: Protein Aminopeptidase N family protein


Mass: 68525.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Idiomarina loihiensis L2TR (bacteria) / Strain: ATCC BAA-735 / DSM 15497 / L2-TR / Gene: IL1258 / Plasmid: pET21_NESG, ILR60-21.5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q5QTY1, membrane alanyl aminopeptidase
#2: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 277 K / Method: microbatch crystallization under oil / pH: 6.8
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 45% PEG/Tacsimate pH 6.8 (Hampton research HR2-092), 45% Silver Bullet (Hampton research HR2- ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 45% PEG/Tacsimate pH 6.8 (Hampton research HR2-092), 45% Silver Bullet (Hampton research HR2-096, G11), 0.1 M sodium citrate., Microbatch crystallization under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.394→50 Å / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.7 % / Biso Wilson estimate: 49.99 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 27.3
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.978 / Mean I/σ(I) obs: 2.05 / Num. unique all: 27765 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.394→42.325 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3489 5.02 %RANDOM
Rwork0.19 ---
obs0.191 69442 99.96 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.973 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 144.29 Å2 / Biso mean: 51.705 Å2 / Biso min: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.12 Å2-0 Å2-0 Å2
2--2.12 Å2-0 Å2
3----4.239 Å2
Refinement stepCycle: LAST / Resolution: 2.394→42.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4709 0 9 222 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064841
X-RAY DIFFRACTIONf_angle_d1.3876580
X-RAY DIFFRACTIONf_chiral_restr0.104717
X-RAY DIFFRACTIONf_plane_restr0.007844
X-RAY DIFFRACTIONf_dihedral_angle_d15.5041742
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.394-2.4270.3561390.33326282767
2.427-2.4610.2691520.29626332785
2.461-2.4980.3361220.28626492771
2.498-2.5370.2711630.26726492812
2.537-2.5790.271260.24826172743
2.579-2.6230.2231250.24926632788
2.623-2.6710.3051220.25126412763
2.671-2.7220.2891560.25426452801
2.722-2.7780.271600.22926042764
2.778-2.8380.3111520.21926082760
2.838-2.9040.2291300.21126712801
2.904-2.9770.2741330.21826322765
2.977-3.0570.2081240.19826562780
3.057-3.1470.2311580.19826252783
3.147-3.2490.2281150.2126702785
3.249-3.3650.2221580.19126002758
3.365-3.50.221440.19726342778
3.5-3.6590.1951390.1826282767
3.659-3.8520.1951690.17726412810
3.852-4.0930.1491320.16426102742
4.093-4.4090.1891300.1526792809
4.409-4.8520.1441110.13326432754
4.852-5.5520.1881380.14926422780
5.552-6.990.1991610.19226282789
6.99-42.3320.1771300.19726572787

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