PDB Short entry for 3FIB HEADER BLOOD COAGULATION 14-JUL-97 3FIB TITLE RECOMBINANT HUMAN GAMMA-FIBRINOGEN CARBOXYL TERMINAL TITLE 2 FRAGMENT (RESIDUES 143-411) BOUND TO CALCIUM AT PH 6.0: A TITLE 3 FURTHER REFINEMENT OF PDB ENTRY 1FIB, AND DIFFERS FROM TITLE 4 1FIB BY THE MODELLING OF A CIS PEPTIDE BOND BETWEEN TITLE 5 RESIDUES K338 AND C339 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBRINOGEN GAMMA CHAIN RESIDUES; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 143 - 411; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BLOOD; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS FIBRINOGEN, BLOOD COAGULATION, FIBRIN POLYMERIZATION, CIS KEYWDS 2 PEPTIDE BONDS EXPDTA X-RAY DIFFRACTION AUTHOR K.P.PRATT,H.C.F.COTE,D.W.CHUNG,R.E.STENKAMP,E.W.DAVIE REVDAT 2 24-FEB-09 3FIB 1 VERSN REVDAT 1 17-SEP-97 3FIB 0 JRNL AUTH K.P.PRATT,H.C.COTE,D.W.CHUNG,R.E.STENKAMP,E.W.DAVIE JRNL TITL THE PRIMARY FIBRIN POLYMERIZATION POCKET: JRNL TITL 2 THREE-DIMENSIONAL STRUCTURE OF A 30-KDA C-TERMINAL JRNL TITL 3 GAMMA CHAIN FRAGMENT COMPLEXED WITH THE PEPTIDE JRNL TITL 4 GLY-PRO-ARG-PRO. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 7176 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9207064 JRNL DOI 10.1073/PNAS.94.14.7176 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.C.YEE,K.P.PRATT,H.CF.COTE,I.LE TRONG,D.W.CHUNG, REMARK 1 AUTH 2 E.W.DAVIE,R.E.STENKAMP,D.C.TELLER REMARK 1 TITL CRYSTAL STRUCTURE OF A 30 KDA C-TERMINAL FRAGMENT REMARK 1 TITL 2 FROM THE GAMMA CHAIN OF HUMAN FIBRINOGEN REMARK 1 REF STRUCTURE V. 5 125 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 11857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 10.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1702 REMARK 3 BIN FREE R VALUE : 0.2318 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1995 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 177 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.77 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAM.CALCIUM REMARK 3 PARAMETER FILE 2 : PARAM.TIPS3P REMARK 3 PARAMETER FILE 3 : PARAMCISPEP.PRO REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPCISPEP.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOLOGY.CALCIUM REMARK 3 TOPOLOGY FILE 3 : TOPOLOGY.TIPS3P REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE WAS NO APPARENT ELECTRON REMARK 3 DENSITY FOR C-TERMINAL RESIDUES 393 - 411. PROTEOLYSIS AT THE REMARK 3 C-TERMINUS WAS CONFIRMED BY MASS SPECTROMETRY. REMARK 4 REMARK 4 3FIB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : AUG-95 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : SIEMENS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XENGEN REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12334 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 33.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 82.7 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.03330 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.1 M MES PH 6.0, REMARK 280 70MM CACL2, SITTING DROP VAPOR DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 34.21000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 392 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 198 -13.80 -160.09 REMARK 500 ASP A 199 -1.01 -154.58 REMARK 500 ASN A 317 85.27 -157.63 REMARK 500 ASN A 337 -93.80 -112.99 REMARK 500 LYS A 338 59.12 -157.37 REMARK 500 ARG A 391 47.18 -90.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 400 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 322 O REMARK 620 2 GLY A 324 O 77.0 REMARK 620 3 HOH A 402 O 89.7 91.7 REMARK 620 4 ASP A 318 OD1 150.5 113.4 116.5 REMARK 620 5 ASP A 318 OD2 155.9 79.7 84.6 48.4 REMARK 620 6 ASP A 320 OD1 82.3 98.6 165.2 69.1 107.6 REMARK 620 7 HOH A 401 O 94.8 171.8 88.9 73.5 108.5 79.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 400 DBREF 3FIB A 144 392 UNP P02679 FIBG_HUMAN 170 418 SEQRES 1 A 249 GLN ILE HIS ASP ILE THR GLY LYS ASP CYS GLN ASP ILE SEQRES 2 A 249 ALA ASN LYS GLY ALA LYS GLN SER GLY LEU TYR PHE ILE SEQRES 3 A 249 LYS PRO LEU LYS ALA ASN GLN GLN PHE LEU VAL TYR CYS SEQRES 4 A 249 GLU ILE ASP GLY SER GLY ASN GLY TRP THR VAL PHE GLN SEQRES 5 A 249 LYS ARG LEU ASP GLY SER VAL ASP PHE LYS LYS ASN TRP SEQRES 6 A 249 ILE GLN TYR LYS GLU GLY PHE GLY HIS LEU SER PRO THR SEQRES 7 A 249 GLY THR THR GLU PHE TRP LEU GLY ASN GLU LYS ILE HIS SEQRES 8 A 249 LEU ILE SER THR GLN SER ALA ILE PRO TYR ALA LEU ARG SEQRES 9 A 249 VAL GLU LEU GLU ASP TRP ASN GLY ARG THR SER THR ALA SEQRES 10 A 249 ASP TYR ALA MET PHE LYS VAL GLY PRO GLU ALA ASP LYS SEQRES 11 A 249 TYR ARG LEU THR TYR ALA TYR PHE ALA GLY GLY ASP ALA SEQRES 12 A 249 GLY ASP ALA PHE ASP GLY PHE ASP PHE GLY ASP ASP PRO SEQRES 13 A 249 SER ASP LYS PHE PHE THR SER HIS ASN GLY MET GLN PHE SEQRES 14 A 249 SER THR TRP ASP ASN ASP ASN ASP LYS PHE GLU GLY ASN SEQRES 15 A 249 CYS ALA GLU GLN ASP GLY SER GLY TRP TRP MET ASN LYS SEQRES 16 A 249 CYS HIS ALA GLY HIS LEU ASN GLY VAL TYR TYR GLN GLY SEQRES 17 A 249 GLY THR TYR SER LYS ALA SER THR PRO ASN GLY TYR ASP SEQRES 18 A 249 ASN GLY ILE ILE TRP ALA THR TRP LYS THR ARG TRP TYR SEQRES 19 A 249 SER MET LYS LYS THR THR MET LYS ILE ILE PRO PHE ASN SEQRES 20 A 249 ARG LEU HET CA A 400 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *177(H2 O) HELIX 1 1 CYS A 153 LYS A 159 1 7 HELIX 2 2 TRP A 208 GLU A 213 1 6 HELIX 3 3 ASN A 230 ALA A 241 1 12 HELIX 4 4 GLU A 270 ASP A 272 5 3 HELIX 5 5 ALA A 289 ASP A 291 5 3 HELIX 6 6 ASP A 301 THR A 305 1 5 HELIX 7 7 CYS A 326 ASP A 330 1 5 SHEET 1 A 7 GLY A 165 ILE A 169 0 SHEET 2 A 7 PHE A 178 ILE A 184 -1 N CYS A 182 O GLY A 165 SHEET 3 A 7 GLY A 190 ARG A 197 -1 N VAL A 193 O TYR A 181 SHEET 4 A 7 LYS A 381 PRO A 388 -1 N ILE A 386 O THR A 192 SHEET 5 A 7 TYR A 244 GLU A 251 -1 N GLU A 251 O LYS A 381 SHEET 6 A 7 THR A 257 ALA A 263 -1 N TYR A 262 O LEU A 246 SHEET 7 A 7 TYR A 280 GLY A 283 -1 N GLY A 283 O ASP A 261 SSBOND 1 CYS A 153 CYS A 182 1555 1555 2.03 SSBOND 2 CYS A 326 CYS A 339 1555 1555 2.03 LINK CA CA A 400 O PHE A 322 1555 1555 2.33 LINK CA CA A 400 O GLY A 324 1555 1555 2.40 LINK CA CA A 400 O HOH A 402 1555 1555 2.44 LINK CA CA A 400 OD1 ASP A 318 1555 1555 2.78 LINK CA CA A 400 OD2 ASP A 318 1555 1555 2.50 LINK CA CA A 400 OD1 ASP A 320 1555 1555 2.51 LINK CA CA A 400 O HOH A 401 1555 1555 2.43 CISPEP 1 LYS A 338 CYS A 339 0 -0.16 SITE 1 AC1 6 ASP A 318 ASP A 320 PHE A 322 GLY A 324 SITE 2 AC1 6 HOH A 401 HOH A 402 CRYST1 37.530 68.420 47.670 90.00 105.36 90.00 P 1 21 1 2 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.026645 0.000000 0.007319 0.00000 SCALE2 0.000000 0.014616 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021755 0.00000