SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" 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.
Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: RESIDUES 328-363 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin
#3: Protein/peptide
HIRUDINI / HIRUGEN
Mass: 1363.399 Da / Num. of mol.: 1 / Fragment: RESIDUES 55-64 / Source method: obtained synthetically Details: THIS POLYPEPTIDE CHAIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE FOR THIS CHAIN OCCURS NATURALLY IN THE C-TERMINAL OF MEDICINAL LEECH(HIRUDO MEDICINALIS). Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P28501, UniProt: P01050*PLUS
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Protein , 1 types, 1 molecules B
#2: Protein
THROMBIN / HUMAN ALPHA THROMBIN / COAGULATION FACTOR II
Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 364-622 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD PLASMA / References: UniProt: P00734, thrombin
Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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Details
Sequence details
RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-GLU1C AND GLY14M-ARG15. RESIDUES THAT ARE MISSING ...RESIDUES THAT ARE MISSING FROM CHAIN A ARE THR1H-GLU1C AND GLY14M-ARG15. RESIDUES THAT ARE MISSING FROM CHAIN B ARE TRP148-LYS149E TYR H 63 IS SULFONATED
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % / Description: NONE
Crystal grow
pH: 7 Details: CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY MACROSEEDING A SOLUTION OF 100MM HEPES PH 7.0, 28% PEG4K,500MM NACL.
Resolution: 1.39→18.55 Å / Num. parameters: 25160 / Num. restraintsaints: 30942 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS ...Details: THE COORDINATES LIST BELOW HAS AMINO ACID NUMBERING FOLLOWING THE CHYMOTRYPSINOGEN NUMBERING SCHEME I.E. A MIXTURE OF SEQUENTIAL NUMBERS AND ALPHABETICAL LETTERS. ASN60G IN CHAIN B IS GLYCOSYLATED. THE MODEL WAS INITIALLY REFINED AGAINST F IN REFMAC-5, THEN FINALLY REFINED AGAINST F(SQUARED) USING SHELXL-97. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.173
3345
5 %
RANDOM
obs
0.118
-
95.9 %
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all
-
67018
-
-
Refine analyze
Num. disordered residues: 10 / Occupancy sum hydrogen: 2233.97 / Occupancy sum non hydrogen: 2739.94
Refinement step
Cycle: LAST / Resolution: 1.39→18.55 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2360
0
35
345
2740
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
s_bond_d
0.012
X-RAY DIFFRACTION
s_angle_d
0.032
X-RAY DIFFRACTION
s_similar_dist
0
X-RAY DIFFRACTION
s_from_restr_planes
0.029
X-RAY DIFFRACTION
s_zero_chiral_vol
0.064
X-RAY DIFFRACTION
s_non_zero_chiral_vol
0.08
X-RAY DIFFRACTION
s_anti_bump_dis_restr
0.042
X-RAY DIFFRACTION
s_rigid_bond_adp_cmpnt
0.004
X-RAY DIFFRACTION
s_similar_adp_cmpnt
0.058
X-RAY DIFFRACTION
s_approx_iso_adps
0.104
+
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