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- PDB-1r8o: Crystal structure of an unusual Kunitz-type trypsin inhibitor fro... -

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Basic information

Entry
Database: PDB / ID: 1r8o
TitleCrystal structure of an unusual Kunitz-type trypsin inhibitor from Copaifera langsdorffii seeds
Components(Kunitz trypsin inhibitor) x 2
KeywordsHYDROLASE INHIBITOR / Kunitz (STI) trypsin inhibitor / beta-trefoil fold / Copaifera langsdorffii
Function / homologySH3 type barrels. - #480 / SH3 type barrels. / Roll / Mainly Beta / : / :
Function and homology information
Biological speciesCopaifera langsdorffii (copaiba)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR QUICK CRIO-SOAKING METHOD / Resolution: 1.83 Å
AuthorsKrauchenco, S. / Nagem, R.A.P. / da Silva, J.A. / Marangoni, S. / Polikarpov, I.
Citation
Journal: Biochimie / Year: 2004
Title: Three-dimensional structure of an unusual Kunitz (STI) type trypsin inhibitor from Copaifera langsdorffii.
Authors: Krauchenco, S. / Nagem, R.A.P. / Da Silva, J.A. / Marangoni, S. / Polikarpov, I.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray diffraction analysis of a novel tryspin inhibitor from seeds of Copaifera langsdorffii
Authors: Krauchenco, S. / Silva, J.A. / Nagem, R.A.P. / Brando Neto, J.R. / Forrer, V.P. / Carmona e Ferreira, R. / Macedo, M.L.R. / Novello, J.C. / Marangoni, S. / Polikarpov, I.
#2: Journal: J.PROTEIN CHEM. / Year: 2001
Title: Biochemical characterization and N-terminal sequences of two new trypsin inhibitors from Copaifera langsdorffii seeds
Authors: da Silva, J.A. / Macedo, M.L.R. / Novello, J.C. / Marangoni, S.
History
DepositionOct 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Kunitz trypsin inhibitor
B: Kunitz trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)18,0322
Polymers18,0322
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-27 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.710, 58.710, 93.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Kunitz trypsin inhibitor / STI


Mass: 10129.670 Da / Num. of mol.: 1 / Fragment: residues 1-96 / Source method: isolated from a natural source / Source: (natural) Copaifera langsdorffii (copaiba) / References: UniProt: P84144
#2: Protein Kunitz trypsin inhibitor / STI


Mass: 7902.113 Da / Num. of mol.: 1 / Fragment: residues 97-167 / Source method: isolated from a natural source / Source: (natural) Copaifera langsdorffii (copaiba) / References: UniProt: P84145
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 25% PEG4000 in 0.1M sodium acetate buffer, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
1,2,31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONLNLS D03B-MX111.54
SYNCHROTRONLNLS D03B-MX121.54
SYNCHROTRONLNLS D03B-MX131.54
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATESep 4, 2000
MARRESEARCH2IMAGE PLATESep 15, 2000
MARRESEARCH3IMAGE PLATESep 18, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1triangular bent crystal monochromatorSINGLE WAVELENGTHMx-ray1
2triangular bent crystal monochromatorSINGLE WAVELENGTHMx-ray1
3triangular bent crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.83→25.28 Å / Num. all: 15027 / Num. obs: 14387 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 23.6
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 3.3 / Num. unique all: 14387 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SIR QUICK CRIO-SOAKING METHOD
Resolution: 1.83→25.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.543 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.131
RfactorNum. reflection% reflectionSelection details
Rfree0.21237 703 5 %RANDOM
Rwork0.16844 ---
all0.17 15027 --
obs0.17 14387 95.7 %-
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: 13.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.83→25.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1267 0 0 182 1449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221293
X-RAY DIFFRACTIONr_angle_refined_deg1.7342.0061736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595165
X-RAY DIFFRACTIONr_chiral_restr0.1340.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02950
X-RAY DIFFRACTIONr_nbd_refined0.2290.2583
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3960.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4640.215
X-RAY DIFFRACTIONr_mcbond_it1.0641.5827
X-RAY DIFFRACTIONr_mcangle_it1.88521332
X-RAY DIFFRACTIONr_scbond_it3.0523466
X-RAY DIFFRACTIONr_scangle_it4.8234.5404
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.83-1.920.267740.2478740.031159487.7
1.92-2.020.244910.2460.026172993.1
2.02-2.140.251840.2350.027177596.9
2.14-2.310.226950.240.023181597.9
2.31-2.540.256870.2310.027178796.5
2.54-2.910.256820.2310.028180595.8
2.91-3.660.2842000.022188198.2
3.66-25.280.2111060.20.02200198.8
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)
11.95740.20120.17742.21910.46912.2555-0.0238-0.10.09450.2637-0.01160.098-0.0235-0.03920.03530.2169-0.0179-0.00170.1962-0.0110.207622.08315.05526.29
22.35050.13010.69632.51970.20792.3870.02170.11180.01070.0364-0.0730.22220.0475-0.05880.05130.1872-0.01-0.00430.2004-0.01340.231917.52511.86818.043
32.5478-0.1620.59392.0010.31172.0187-0.01690.01160.11090.0943-0.00460.1895-0.06070.00310.02150.135-0.01510.00860.1193-0.00390.158720.19714.3321.611
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 96
2X-RAY DIFFRACTION2B97 - 167
3X-RAY DIFFRACTION3A97 - 189
4X-RAY DIFFRACTION3B168 - 255

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