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- PDB-3ig4: Structure of a putative aminopeptidase P from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3ig4
TitleStructure of a putative aminopeptidase P from Bacillus anthracis
ComponentsXaa-pro aminopeptidase
KeywordsHYDROLASE / aminopeptidase / bacillus anthracis / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


metalloaminopeptidase activity / manganese ion binding / proteolysis
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Aminopeptidase P family protein / Putative xaa-pro aminopeptidase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.89 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Structure of a putative aminopeptidase P from Bacillus anthracis
Authors: Anderson, S.M. / Wawrzak, Z. / Skarina, T. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 14, 2011Group: Database references / Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-pro aminopeptidase
B: Xaa-pro aminopeptidase
C: Xaa-pro aminopeptidase
D: Xaa-pro aminopeptidase
E: Xaa-pro aminopeptidase
F: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,43656
Polymers296,1266
Non-polymers4,31050
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32340 Å2
ΔGint-792 kcal/mol
Surface area100430 Å2
MethodPISA
2
A: Xaa-pro aminopeptidase
C: Xaa-pro aminopeptidase
E: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,21828
Polymers148,0633
Non-polymers2,15525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-361 kcal/mol
Surface area56540 Å2
MethodPISA
3
B: Xaa-pro aminopeptidase
D: Xaa-pro aminopeptidase
F: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,21828
Polymers148,0633
Non-polymers2,15525
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9760 Å2
ΔGint-360 kcal/mol
Surface area56640 Å2
MethodPISA
4
A: Xaa-pro aminopeptidase
B: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,27320
Polymers98,7092
Non-polymers1,56518
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-218 kcal/mol
Surface area37360 Å2
MethodPISA
5
C: Xaa-pro aminopeptidase
D: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,17719
Polymers98,7092
Non-polymers1,46917
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-208 kcal/mol
Surface area37170 Å2
MethodPISA
6
E: Xaa-pro aminopeptidase
F: Xaa-pro aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,98517
Polymers98,7092
Non-polymers1,27615
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-216 kcal/mol
Surface area37280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.88, 180.88, 254.78
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 419
2111B1 - 419
3111C1 - 419
4111D1 - 419
5111E1 - 419
6111F1 - 419

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Components

#1: Protein
Xaa-pro aminopeptidase


Mass: 49354.324 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS1763, BA_1901, GBAA1901, GBAA_1901 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81RY4, UniProt: A0A6L8PS06*PLUS
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: SO4

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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: 3.52 Å3/Da / Density % sol: 65.04 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate, 5% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2009 / Details: beryllium lense
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.89→50 Å / Num. obs: 94533 / % possible obs: 99.8 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 2.7 / Redundancy: 12.7 % / Rmerge(I) obs: 0.125 / Χ2: 1.067 / Net I/σ(I): 19
Reflection shellResolution: 2.89→3 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8934 / Χ2: 1.003 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
BLU-MAXdata collection
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.89→44.4 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.197 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.86 / SU B: 26.656 / SU ML: 0.237 / SU R Cruickshank DPI: 0.953 / SU Rfree: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.953 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4743 5 %RANDOM
Rwork0.198 ---
all0.199 94923 --
obs0.199 94533 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 149.67 Å2 / Biso mean: 46.921 Å2 / Biso min: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å20 Å2
2---0.19 Å2-0 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.89→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20274 0 202 0 20476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02220887
X-RAY DIFFRACTIONr_angle_refined_deg0.9461.96228238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.69452524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.36325.4961039
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.653153809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3891566
X-RAY DIFFRACTIONr_chiral_restr0.0650.23110
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215600
X-RAY DIFFRACTIONr_mcbond_it1.371.512510
X-RAY DIFFRACTIONr_mcangle_it2.839220280
X-RAY DIFFRACTIONr_scbond_it4.59738377
X-RAY DIFFRACTIONr_scangle_it7.8334.57950
Refine LS restraints NCS

Ens-ID: 1 / Number: 3344 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.130.05
2BTIGHT POSITIONAL0.110.05
3CTIGHT POSITIONAL0.110.05
4DTIGHT POSITIONAL0.120.05
5ETIGHT POSITIONAL0.130.05
6FTIGHT POSITIONAL0.140.05
1ATIGHT THERMAL0.370.5
2BTIGHT THERMAL0.360.5
3CTIGHT THERMAL0.330.5
4DTIGHT THERMAL0.370.5
5ETIGHT THERMAL0.410.5
6FTIGHT THERMAL0.340.5
LS refinement shellResolution: 2.89→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 324 -
Rwork0.292 6280 -
all-6604 -
obs-6478 96.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5578-0.0556-0.01650.2818-0.07830.2554-0.07940.0815-0.19420.04210.0870.03870.0250.012-0.00760.2259-0.00490.03310.14140.00510.080656.85253.84471.926
20.3544-0.02320.00690.1461-0.01790.1549-0.0308-0.017-0.1651-0.03270.01150.02670.07390.09360.01930.2229-0.00990.01720.12160.01910.083556.90453.77771.848
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 169
2X-RAY DIFFRACTION1B5 - 169
3X-RAY DIFFRACTION1C5 - 169
4X-RAY DIFFRACTION1D5 - 169
5X-RAY DIFFRACTION1E5 - 169
6X-RAY DIFFRACTION1F5 - 169
7X-RAY DIFFRACTION2A170 - 412
8X-RAY DIFFRACTION2B170 - 412
9X-RAY DIFFRACTION2C170 - 412
10X-RAY DIFFRACTION2D170 - 412
11X-RAY DIFFRACTION2E170 - 412
12X-RAY DIFFRACTION2F170 - 412

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