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- PDB-3pro: ALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION -

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Basic information

Entry
Database: PDB / ID: 3pro
TitleALPHA-LYTIC PROTEASE COMPLEXED WITH C-TERMINAL TRUNCATED PRO REGION
Components(ALPHA-LYTIC PROTEASE) x 2
Keywordshydrolase/hydrolase inhibitor / PRO REGION / FOLDASE / PROTEIN FOLDING / SERINE PROTEASE / hydrolase-hydrolase inhibitor complex
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 / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 26, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2012Group: Non-polymer description
Revision 1.4Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7086
Polymers75,3024
Non-polymers4062
Water5,783321
1
A: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8543
Polymers37,6512
Non-polymers2031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-10 kcal/mol
Surface area13900 Å2
MethodPISA
2
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8543
Polymers37,6512
Non-polymers2031
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-8 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 101.000, 72.140
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9972, -0.069044, -0.028735), (0.068494, 0.997457, -0.01972), (0.030023, 0.017697, 0.999392)
Vector: 15.57713, 50.66458, 12.83321)

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Components

#1: Protein ALPHA-LYTIC PROTEASE


Mass: 19815.014 Da / Num. of mol.: 2 / Fragment: MATURE PROTEASE / Mutation: M158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Cell line: B834 / Plasmid: PT7PRO-3 / Cellular location (production host): CULTURE FILTRATE / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P00778
#2: Protein ALPHA-LYTIC PROTEASE


Mass: 17835.881 Da / Num. of mol.: 2 / 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-3 / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) PLYSS / References: UniProt: P00778
#3: Chemical ChemComp-AES / 4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / AEBSF


Mass: 203.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10FNO2S / Comment: protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.79 Å3/Da / Density % sol: 56 %
Description: STATISTICS INCLUDE 78512 MEASUREMENTS MADE ON ROTATING ANODE SOURCE
Crystal growpH: 6.25 / Details: pH 6.25
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 7 ℃ / pH: 8 / 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: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 5, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→67.4 Å / Num. obs: 255283 / % possible obs: 96.5 % / Redundancy: 3.46 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.6 / % possible all: 95.5
Reflection
*PLUS
Num. obs: 73741 / Num. measured all: 176771
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.854refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TAL

1tal


Resolution: 1.8→67.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 -10 %RANDOM
Rwork0.207 ---
obs0.207 73722 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.8→67.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5018 0 24 321 5363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.2
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: 1.8→1.81 Å / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.25 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.854 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

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