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- PDB-2spt: DIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROM... -

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Basic information

Entry
Database: PDB / ID: 2spt
TitleDIFFERENCES IN THE METAL ION STRUCTURE BETWEEN SR-AND CA-PROTHROMBIN FRAGMENT 1
ComponentsPROTHROMBINThrombin
KeywordsHYDROLASE(SERINE PROTEINASE)
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / 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. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
STRONTIUM ION / Prothrombin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTulinsky, A.
Citation
Journal: Biochemistry / Year: 1994
Title: Differences in the metal ion structure between Sr- and Ca-prothrombin fragment 1.
Authors: Seshadri, T.P. / Skrzypczak-Jankun, E. / Yin, M. / Tulinsky, A.
#1: Journal: Biochemistry / Year: 1992
Title: The Ca2+ Ion and Membrane Binding Structure of the Gla Domain of Ca-Prothrombin Fragment 1
Authors: Soriano-Garcia, M. / Padmanabhan, K. / De Vos, A.M. / Tulinsky, A.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Structure of Bovine Prothrombin Fragment 1 Refined at 2.25 Angstroms Resolution
Authors: Seshadri, T.P. / Tulinsky, A. / Skrzypczak-Jankun, E. / Park, C.H.
History
DepositionFeb 1, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,65110
Polymers16,7291
Non-polymers9229
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.690, 54.120, 131.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 54 / 2: CIS PROLINE - PRO 95

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Components

#1: Protein PROTHROMBIN / Thrombin


Mass: 16729.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P00735, thrombin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: THRB_BOVIN SWISS-PROT PDB SEQRES COMMENT GLU 50 CGU 7 GAMMA-CARBOXY-GLUTAMIC ACID GLU 51 CGU 8 GAMMA-CARBOXY-GLUTAMIC ACID GLU 58 CGU 15 GAMMA-CARBOXY-GLUTAMIC ACID GLU 60 CGU 17 GAMMA-CARBOXY-GLUTAMIC ACID GLU 63 CGU 20 GAMMA-CARBOXY-GLUTAMIC ACID GLU 64 CGU 21 GAMMA-CARBOXY-GLUTAMIC ACID GLU 69 CGU 26 GAMMA-CARBOXY-GLUTAMIC ACID GLU 70 CGU 27 GAMMA-CARBOXY-GLUTAMIC ACID GLU 73 CGU 30 GAMMA-CARBOXY-GLUTAMIC ACID GLU 76 CGU 33 GAMMA-CARBOXY-GLUTAMIC ACID

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.77 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Details: taken from Soriano-Garacia, M. et al (1989), Biochemistry, 28, 6805-6810.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 Mcacodylate1drop
28 %(w/v)PEG60001drop
3100 M1dropCa2+
40.1 Mcacodylate1reservoir
516 %(w/v)PEG60001reservoir
6200 M1reservoirCa2+

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. all: 10366 / Num. obs: 5331

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Processing

Software
NameClassification
PROFFTrefinement
PROLSQrefinement
RefinementResolution: 2.5→7 Å /
RfactorNum. reflection
obs0.167 4812
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1158 0 22 90 1270
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.050.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.51.2
X-RAY DIFFRACTIONp_mcangle_it0.91.5
X-RAY DIFFRACTIONp_scbond_it0.81.5
X-RAY DIFFRACTIONp_scangle_it1.42
X-RAY DIFFRACTIONp_plane_restr0.0160.03
X-RAY DIFFRACTIONp_chiral_restr0.0170.15
X-RAY DIFFRACTIONp_singtor_nbd0.250.5
X-RAY DIFFRACTIONp_multtor_nbd0.330.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.330.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor23
X-RAY DIFFRACTIONp_staggered_tor2415
X-RAY DIFFRACTIONp_orthonormal_tor2920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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