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- PDB-4pro: ALPHA-LYTIC PROTEASE COMPLEXED WITH PRO REGION -

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Basic information

Entry
Database: PDB / ID: 4pro
TitleALPHA-LYTIC PROTEASE COMPLEXED WITH PRO REGION
Components(ALPHA-LYTIC PROTEASEAlpha-lytic endopeptidase) x 2
KeywordsSERINE PROTEASE / PRO REGION / FOLDASE / PROTEIN FOLDING
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
Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionOct 1, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 22, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_prop.biol_id
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
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
C: ALPHA-LYTIC PROTEASE
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)75,3024
Polymers75,3024
Non-polymers00
Water1,24369
1
A: ALPHA-LYTIC PROTEASE
C: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)37,6512
Polymers37,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-18 kcal/mol
Surface area14080 Å2
MethodPISA
2
B: ALPHA-LYTIC PROTEASE
D: ALPHA-LYTIC PROTEASE


Theoretical massNumber of molelcules
Total (without water)37,6512
Polymers37,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-15 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.800, 61.900, 72.600
Angle α, β, γ (deg.)109.40, 99.20, 102.40
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.778697, 0.440619, 0.446638), (0.429057, -0.893387, 0.133302), (0.457756, 0.087831, -0.884729)
Vector: -20.37255, 26.29845, 54.59003)

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Components

#1: Protein ALPHA-LYTIC PROTEASE / Alpha-lytic endopeptidase


Mass: 19815.014 Da / Num. of mol.: 2
Fragment: CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION
Mutation: CHAIN A, B, M158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Fragment: CHAIN C, D / Gene: T7 / Plasmid: PT7PRO / Cellular location (production host): INCLUSION BODIES / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00778
#2: Protein ALPHA-LYTIC PROTEASE / Alpha-lytic endopeptidase


Mass: 17835.881 Da / Num. of mol.: 2
Fragment: CHAIN A, B, MATURE PROTEASE. CHAIN C, D, PRO REGION
Mutation: CHAIN A, B, M158A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lysobacter enzymogenes (bacteria) / Fragment: CHAIN C, D / Gene: T7 / Plasmid: PT7PRO / Cellular location (production host): INCLUSION BODIES / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P00778
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: pH 6.5
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: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 18, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→28.2 Å / Num. obs: 104427 / % possible obs: 95.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.5
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.4 / % possible all: 93.9
Reflection
*PLUS
Num. obs: 31304 / Num. measured all: 104427
Reflection shell
*PLUS
% possible obs: 93.9 %

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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 3PRO

3pro


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 -10 %RANDOM
Rwork0.191 ---
obs0.191 31292 95.9 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.706 Å2-0.216 Å2-0.959 Å2
2---2.001 Å22.139 Å2
3---3.707 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 0 69 5086
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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: 2.4→2.42 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.299 / Total num. of bins used: 50
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2

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