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- PDB-2pro: PRO REGION OF ALPHA-LYTIC PROTEASE -

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Basic information

Entry
Database: PDB / ID: 2pro
TitlePRO REGION OF ALPHA-LYTIC PROTEASE
ComponentsALPHA-LYTIC PROTEASE
KeywordsPRO REGION / FOLDASE / PROTEIN FOLDING / SERINE PROTEASE
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #50 / Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / GMP Synthetase; Chain A, domain 3 / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain ...GMP Synthetase; Chain A, domain 3 - #50 / Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / GMP Synthetase; Chain A, domain 3 / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsSauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: Structure of alpha-lytic protease complexed with its pro region.
Authors: Sauter, N.K. / Mau, T. / Rader, S.D. / Agard, D.A.
History
DepositionAug 20, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LYTIC PROTEASE
B: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)53,5083
Polymers53,5083
Non-polymers00
Water00
1
A: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)17,8361
Polymers17,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)17,8361
Polymers17,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)17,8361
Polymers17,8361
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
A: ALPHA-LYTIC PROTEASE

B: ALPHA-LYTIC PROTEASE

C: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)53,5083
Polymers53,5083
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation1_454x-1,y,z-11
Buried area2840 Å2
ΔGint-24 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.600, 54.700, 64.000
Angle α, β, γ (deg.)104.00, 102.50, 91.90
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.24397, -0.435926, 0.866283), (0.968271, -0.159353, 0.192504), (0.054127, 0.885762, 0.460972)-1.136, 55.37418, 1.91559
2given(-0.406173, 0.913113, -0.035342), (-0.344144, -0.117025, 0.931596), (0.846516, 0.390551, 0.361775)-20.04315, 41.34668, 45.73866

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Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 17835.881 Da / Num. of mol.: 3 / Fragment: PRO REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Description: T7 EXPRESSION SYSTEM / Cell line: B834 / Plasmid: PT7PRO / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P00778
Sequence detailsTHE FIVE METHIONINE RESIDUES IN THIS ENTRY ARE ACTUALLY A MIXTURE OF ABOUT 80% SELENO-L-METHIONINE ...THE FIVE METHIONINE RESIDUES IN THIS ENTRY ARE ACTUALLY A MIXTURE OF ABOUT 80% SELENO-L-METHIONINE AND 20% L-METHIONINE.

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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: 2.94 Å3/Da / Density % sol: 58 % / Description: DATA WERE COLLECTED WITH INVERSE BEAM GEOMETRY
Crystal growpH: 8 / Details: pH 8.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 7 ℃ / Method: vapor diffusion / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
20.34 Mlithium sulfate1drop
32.3 %glycerol1drop
42 mMdithiothreitol1drop
52.7 mMMES1drop
615 mMcitric acid1reservoirbufferA
730 mMphosphoric acid1reservoirbufferA
826 mMorthoboric acid1reservoirbufferA
90.155 Msodium hydroxide1reservoirbufferA
100.8 Mlithium sulfate1reservoirbufferA
115 %glycerol1reservoirbufferA
12bufferA1drop0.45 times

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9690, 0.97915, 0.97938
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Mar 23, 1996
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9691
20.979151
30.979381
ReflectionResolution: 3→16 Å / Num. obs: 22778 / % possible obs: 93.5 % / Redundancy: 1.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 13
Reflection shellResolution: 3→3.14 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 3.4 / % possible all: 94.9
Reflection
*PLUS
Num. measured all: 39904
Reflection shell
*PLUS
% possible obs: 94.9 %

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.854refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3→6 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.342 -10 %RANDOM
Rwork0.202 ---
obs0.202 10068 93.5 %-
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 0 0 3139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.12 Å / Rfactor Rfree: 0.489 / Rfactor Rwork: 0.314 / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2PARAMETER.ELEMENTS

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