HEADER BLOOD CLOTTING 22-MAR-05 1Z6C TITLE SOLUTION STRUCTURE OF AN EGF PAIR (EGF34) FROM VITAMIN K-DEPENDENT TITLE 2 PROTEIN S COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN K-DEPENDENT PROTEIN S; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EGF MODULES 3 AND 4; 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 GENE: PROS1, PROS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS EGF MODULE, BLOOD CLOTTING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.DRAKENBERG,H.GHASRIANI,E.THULIN,A.M.THAMLITZ,A.MURANYI,A.ANNILA, AUTHOR 2 J.STENFLO REVDAT 5 16-OCT-24 1Z6C 1 REMARK REVDAT 4 02-MAR-22 1Z6C 1 REMARK REVDAT 3 28-APR-09 1Z6C 1 REMARK REVDAT 2 24-FEB-09 1Z6C 1 VERSN REVDAT 1 21-JUN-05 1Z6C 0 JRNL AUTH T.DRAKENBERG,H.GHASRIANI,E.THULIN,A.MURANYI,A.ANNILA, JRNL AUTH 2 J.STENFLO JRNL TITL SOLUTION STRUCTURE OF THE CA(2+)-BINDING EGF3-4 PAIR FROM JRNL TITL 2 VITAMIN K-DEPENDENT PROTEIN S: IDENTIFICATION OF AN UNUSUAL JRNL TITL 3 FOLD IN EGF3. JRNL REF BIOCHEMISTRY V. 44 8782 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15952784 JRNL DOI 10.1021/BI050101F REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER (CNS), REMARK 3 BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE,JIANG,KUSZEWSKI, REMARK 3 NILGES, PANNU,READ,RICE,SIMONSON,WARREN (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 912 RESTRAINTS, 756 NOE RESTRAINTS, 76 TORSION ANGLE RESTRAINTS, REMARK 3 46 RESIDUAL DIPOLAR COUPLINGS AND 30 RESTRAINTS FROM HYDROGEN REMARK 3 BONDS REMARK 4 REMARK 4 1Z6C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032353. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 309; 309; 309 REMARK 210 PH : 6.0; 6.0; 6.0 REMARK 210 IONIC STRENGTH : LOW; LOW; LOW REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM EGF34 U-15N; PH 6.0; 0.1MM REMARK 210 NAN3; 1MM DSS; 10MM CACL2; 0.5 REMARK 210 MM EGF34 U-15N; PHAGE PF1 16 MG/ REMARK 210 ML; PH 6.0; 10MM CACL2; 1MM REMARK 210 EGF34; PH 6.0; 0.1 MM NAN3; 1MM REMARK 210 DSS; 10 MM CACL2 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D REMARK 210 NOESY; IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 5.1, SPARKY 3.1, FELIX 97 REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 202 O HOH A 249 1.63 REMARK 500 OE1 GLU A 205 OD1 ASN A 217 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP A 160 -82.84 -124.91 REMARK 500 1 ASP A 162 102.25 44.25 REMARK 500 1 GLU A 163 -75.38 -107.70 REMARK 500 1 SER A 169 99.56 -160.16 REMARK 500 1 ILE A 170 -78.73 -95.45 REMARK 500 1 CYS A 171 33.53 -148.58 REMARK 500 1 THR A 173 47.74 37.86 REMARK 500 1 ALA A 174 -79.92 -79.19 REMARK 500 1 VAL A 175 54.27 -144.30 REMARK 500 1 ASP A 182 -171.68 -175.37 REMARK 500 1 PRO A 188 149.70 -35.45 REMARK 500 1 GLU A 189 -142.98 35.04 REMARK 500 1 ASP A 202 149.04 -38.96 REMARK 500 1 ASP A 204 59.08 -103.46 REMARK 500 1 ASN A 209 61.75 160.99 REMARK 500 1 ALA A 212 -90.81 -88.71 REMARK 500 1 PRO A 219 96.12 -47.32 REMARK 500 1 TYR A 225 -145.59 -108.74 REMARK 500 1 CYS A 226 -81.49 -159.89 REMARK 500 1 ASP A 227 59.85 18.76 REMARK 500 1 PHE A 232 -125.56 -140.83 REMARK 500 1 ALA A 235 -173.60 -51.07 REMARK 500 1 LYS A 239 -44.48 -159.07 REMARK 500 2 ASP A 160 -84.15 -108.79 REMARK 500 2 ASP A 162 101.14 47.95 REMARK 500 2 GLU A 163 -101.33 -106.75 REMARK 500 2 SER A 169 96.19 -160.21 REMARK 500 2 ILE A 170 -75.70 -100.16 REMARK 500 2 THR A 173 45.43 35.79 REMARK 500 2 ALA A 174 -75.08 -79.87 REMARK 500 2 VAL A 175 27.08 -155.25 REMARK 500 2 ASP A 182 -171.87 179.69 REMARK 500 2 PRO A 188 59.76 -52.66 REMARK 500 2 GLU A 189 -166.83 114.49 REMARK 500 2 ASP A 204 57.89 -101.09 REMARK 500 2 ASN A 209 75.99 28.60 REMARK 500 2 GLN A 213 -78.00 -106.91 REMARK 500 2 PRO A 219 99.04 -48.75 REMARK 500 2 TYR A 222 -178.69 -67.30 REMARK 500 2 CYS A 226 -166.32 -116.00 REMARK 500 2 ASP A 227 96.59 59.73 REMARK 500 2 PHE A 232 -133.38 -122.75 REMARK 500 2 ALA A 235 -178.78 -50.78 REMARK 500 2 ASP A 237 -75.70 -51.19 REMARK 500 2 GLN A 238 -53.29 152.02 REMARK 500 2 CYS A 241 111.34 -160.86 REMARK 500 3 ASP A 160 -80.35 -117.73 REMARK 500 3 ASP A 162 91.18 46.55 REMARK 500 3 GLU A 163 -85.99 -100.06 REMARK 500 3 SER A 169 69.97 -159.53 REMARK 500 REMARK 500 THIS ENTRY HAS 436 RAMACHANDRAN OUTLIERS. 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 246 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 160 OD1 REMARK 620 2 VAL A 161 O 77.6 REMARK 620 3 ASP A 162 O 128.0 51.4 REMARK 620 4 GLU A 163 OE1 97.4 67.6 57.5 REMARK 620 5 ASN A 178 OD1 151.5 124.4 73.4 78.2 REMARK 620 6 ILE A 179 O 107.6 160.1 123.7 128.9 58.7 REMARK 620 7 HOH A 248 O 78.9 79.8 98.9 147.1 119.7 82.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 247 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 202 OD2 REMARK 620 2 ILE A 203 O 75.5 REMARK 620 3 GLU A 205 OE1 135.6 61.0 REMARK 620 4 ASN A 217 OD1 120.4 89.0 54.6 REMARK 620 5 TYR A 218 O 106.0 166.6 114.4 78.8 REMARK 620 6 HOH A 249 O 39.4 62.4 106.5 82.2 109.9 REMARK 620 N 1 2 3 4 5 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 246 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 247 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4729 RELATED DB: BMRB DBREF 1Z6C A 159 245 UNP P07225 PROS_HUMAN 200 286 SEQRES 1 A 87 LYS ASP VAL ASP GLU CYS SER LEU LYS PRO SER ILE CYS SEQRES 2 A 87 GLY THR ALA VAL CYS LYS ASN ILE PRO GLY ASP PHE GLU SEQRES 3 A 87 CYS GLU CYS PRO GLU GLY TYR ARG TYR ASN LEU LYS SER SEQRES 4 A 87 LYS SER CYS GLU ASP ILE ASP GLU CYS SER GLU ASN MET SEQRES 5 A 87 CYS ALA GLN LEU CYS VAL ASN TYR PRO GLY GLY TYR THR SEQRES 6 A 87 CYS TYR CYS ASP GLY LYS LYS GLY PHE LYS LEU ALA GLN SEQRES 7 A 87 ASP GLN LYS SER CYS GLU VAL VAL SER HET CA A 246 1 HET CA A 247 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) FORMUL 4 HOH *2(H2 O) HELIX 1 1 ASP A 204 ASN A 209 1 6 SHEET 1 A 2 ARG A 192 ASN A 194 0 SHEET 2 A 2 SER A 199 GLU A 201 -1 O GLU A 201 N ARG A 192 SHEET 1 B 2 LEU A 214 CYS A 215 0 SHEET 2 B 2 CYS A 224 TYR A 225 -1 O TYR A 225 N LEU A 214 SSBOND 1 CYS A 164 CYS A 176 1555 1555 2.03 SSBOND 2 CYS A 171 CYS A 185 1555 1555 2.03 SSBOND 3 CYS A 187 CYS A 200 1555 1555 2.03 SSBOND 4 CYS A 206 CYS A 215 1555 1555 2.03 SSBOND 5 CYS A 211 CYS A 224 1555 1555 2.02 SSBOND 6 CYS A 226 CYS A 241 1555 1555 2.03 LINK OD1 ASP A 160 CA CA A 246 1555 1555 2.43 LINK O VAL A 161 CA CA A 246 1555 1555 2.61 LINK O ASP A 162 CA CA A 246 1555 1555 2.73 LINK OE1 GLU A 163 CA CA A 246 1555 1555 2.43 LINK OD1 ASN A 178 CA CA A 246 1555 1555 2.43 LINK O ILE A 179 CA CA A 246 1555 1555 2.64 LINK OD2 ASP A 202 CA CA A 247 1555 1555 2.41 LINK O ILE A 203 CA CA A 247 1555 1555 2.66 LINK OE1 GLU A 205 CA CA A 247 1555 1555 2.45 LINK OD1 ASN A 217 CA CA A 247 1555 1555 2.28 LINK O TYR A 218 CA CA A 247 1555 1555 2.72 LINK CA CA A 246 O HOH A 248 1555 1555 2.44 LINK CA CA A 247 O HOH A 249 1555 1555 2.44 SITE 1 AC1 4 ASP A 160 GLU A 163 ASN A 178 ILE A 179 SITE 1 AC2 4 ASP A 202 GLU A 205 ASN A 217 TYR A 218 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1