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 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
(ATOM LINES ARE NOT SHOWN.)
END
