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- PDB-4b2a: Structure of the factor Xa-like trypsin variant triple-Ala (TGA) ... -

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Basic information

Entry
Database: PDB / ID: 4b2a
TitleStructure of the factor Xa-like trypsin variant triple-Ala (TGA) in complex with eglin C
Components
  • CATIONIC TRYPSIN
  • EGLIN C
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / response to wounding / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. ...Trypsin Inhibitor V, subunit A / Proteinase inhibitor I13, potato inhibitor I / Proteinase inhibitor I13, potato inhibitor I superfamily / Potato inhibitor I family / Potato inhibitor I family signature. / Trypsin Inhibitor V; Chain A / : / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / 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
Serine protease 1 / Eglin C
Similarity search - Component
Biological speciesBOS TAURUS (domestic cattle)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsMenzel, A. / Neumann, P. / Stubbs, M.T.
CitationJournal: Biol.Chem. / Year: 2014
Title: Thermodynamic signatures in macromolecular interactions involving conformational flexibility.
Authors: Menzel, A. / Neumann, P. / Schwieger, C. / Stubbs, M.T.
History
DepositionJul 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Jul 23, 2014Group: Database references
Revision 1.4May 8, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATIONIC TRYPSIN
B: EGLIN C
C: CATIONIC TRYPSIN
D: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,55810
Polymers62,1404
Non-polymers4196
Water2,414134
1
A: CATIONIC TRYPSIN
B: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3566
Polymers31,0702
Non-polymers2864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: CATIONIC TRYPSIN
D: EGLIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2024
Polymers31,0702
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.800, 35.110, 105.390
Angle α, β, γ (deg.)90.00, 104.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.931406, -0.113444, 0.345851), (0.08973, -0.992428, -0.083881), (0.352748, -0.047094, 0.934533)-10.03978, 3.94177, 42.86353
3given(-0.935727, -0.075585, 0.344533), (0.051349, -0.995555, -0.078948), (0.348969, -0.056182, 0.935449)-9.83567, 3.9084, 42.78361

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein CATIONIC TRYPSIN / BETA-TRYPSIN / ALPHA-TRYPSIN CHAIN 1 / ALPHA-TRYPSIN CHAIN 2


Mass: 23388.371 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (domestic cattle) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00760, trypsin
#2: Protein EGLIN C


Mass: 7681.588 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-70 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIRUDO MEDICINALIS (medicinal leech) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01051

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Non-polymers , 4 types, 140 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.61 Å3/Da / Density % sol: 52.52 % / Description: NONE
Crystal growTemperature: 283 K
Details: 18% (W/V) PEG 10,000, 20% (V/V) GLYCEROL, 100 MM TRIS-HCL PH 8.5 AND 100 MM NACL AT 283 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 16, 2008 / Details: MIRRORS
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 44709 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.9
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2 / % possible all: 92.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1V2L, 1ACB

1v2l

1acb


Resolution: 1.89→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.734 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25898 1152 2.6 %RANDOM
Rwork0.2031 ---
obs0.2045 43498 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.077 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å21.7 Å2
2--2.27 Å20 Å2
3---0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.89→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4360 0 24 134 4518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.024488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9476099
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0995574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12724.831178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56115704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7561512
X-RAY DIFFRACTIONr_chiral_restr0.1340.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213388
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 339 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Rms dev position: 2.12 Å / Weight position: 1.5

Dom-IDAuth asym-ID
1A
2C
LS refinement shellResolution: 1.896→1.945 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 85 -
Rwork0.333 2646 -
obs--85.42 %
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)
12.62780.0075-0.51671.5142-1.23922.19-0.0086-0.2033-0.0588-0.0353-0.1481-0.27560.02940.19130.15680.0861-0.0013-0.02720.03610.0160.1167-21.622314.9852-4.9804
23.429-0.0389-1.64920.76540.40233.92870.0760.3629-0.01120.0119-0.06210.1471-0.0198-0.3038-0.01380.1448-0.0151-0.0140.05380.01180.1137-5.164-7.4817-49.6342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 245
2X-RAY DIFFRACTION1B5 - 70
3X-RAY DIFFRACTION2C16 - 245
4X-RAY DIFFRACTION2D5 - 70

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