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- PDB-3pmb: 2.9 Angstrom crystal structure of bovine thrombin in tetragonal s... -

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Basic information

Entry
Database: PDB / ID: 3pmb
Title2.9 Angstrom crystal structure of bovine thrombin in tetragonal spacegroup
Components
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / Protease / Thrombosis / Fibrinolosys
Function / homology
Function and homology information


fibrinogen binding / protein polymerization / thrombin / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / proteolysis / serine-type endopeptidase activity / calcium ion binding / extracellular space
Similarity search - Function
Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. ...Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Prothrombin/thrombin / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Vitamin K-dependent carboxylation domain. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Gamma-carboxyglutamic acid-rich (GLA) domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWright, H.T. / Scarsdale, J.N. / Desai, B.J.
CitationJournal: Biochemistry / Year: 2011
Title: Interaction of thrombin with sucrose octasulfate.
Authors: Desai, B.J. / Boothello, R.S. / Mehta, A.Y. / Scarsdale, J.N. / Wright, H.T. / Desai, U.R.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5476
Polymers66,5014
Non-polymers462
Water1,33374
1
A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2733
Polymers33,2502
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-25 kcal/mol
Surface area12050 Å2
MethodPISA
2
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2733
Polymers33,2502
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-20 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)87.644, 87.644, 194.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21D

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Components

#1: Protein/peptide Thrombin light chain /


Mass: 3477.845 Da / Num. of mol.: 2 / Fragment: Bovine Thrombin Light Chain residues 336-364 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#2: Protein Thrombin heavy chain /


Mass: 29772.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.81 Å3/Da / Density % sol: 56.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 3 microliters Bovine thrombin, 7 mg/ml in 0.01M Tris-HCl, ph 8.0, 0.05M NaCl, 0.1M sodium citrate, 20% w/v PEG3350, 15% v/v 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 22, 2008 / Details: Rigaku Varimax Confocal Optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→39.2 Å / Num. all: 19432 / Num. obs: 16696 / % possible obs: 85.9 % / Redundancy: 4.19 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.62 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 4.3 / Num. unique all: 1887 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
REFMAC5.5.0109refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.805 / SU B: 40.628 / SU ML: 0.349
Isotropic thermal model: DOMAIN LEVEL TLS, RESIDUAL ISOTROPIC B FACTORS
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30068 746 5.1 %RANDOM
Rwork0.24201 ---
obs0.24499 14714 84.6 %-
all-17545 --
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: 35.286 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å20 Å2
2---1.07 Å20 Å2
3---2.15 Å2
Refine analyzeLuzzati coordinate error obs: 0.442 Å
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 2 74 4331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224379
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9545954
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8315542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33123.636198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.73315697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9521531
X-RAY DIFFRACTIONr_chiral_restr0.0770.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213361
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_it0.2461.52722
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45924344
X-RAY DIFFRACTIONr_scbond_it0.50431657
X-RAY DIFFRACTIONr_scangle_it0.8914.51610
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
816tight positional0.080.05
745loose positional0.25
816tight thermal0.080.5
745loose thermal0.0810
LS refinement shellResolution: 2.9→2.972 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 71 -
Rwork0.289 1113 -
obs--96.18 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.27710.6205-0.50273.1490.62551.3772-0.05710.2796-0.22990.07070.01-0.17640.11460.01150.0470.07750.0229-0.03350.1399-0.11090.111-4.2715-21.514931.8908
22.27580.49650.23562.0296-0.48091.7771-0.06030.33690.1504-0.0992-0.03920.042-0.03430.07590.09950.0212-0.0029-0.00570.13430.08110.05911.9984-66.833831.3999
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION1B16 - 243
3X-RAY DIFFRACTION2C1 - 15
4X-RAY DIFFRACTION2D16 - 243

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