HEADER BLOOD CLOTTING 18-AUG-23 8TVL TITLE PLASMINOGEN BINDING GROUP A STREPTOCOCCUS M-LIKE PROTEIN FROM AP53 TITLE 2 BOUND TO HUMAN PLASMINOGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMINOGEN-BINDING GROUP A STREPTOCOCCAL M-LIKE PROTEIN COMPND 3 PAM; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 STRAIN: AP53; SOURCE 5 GENE: PAM, EMM; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK293T KEYWDS PAM, HUMAN PLASMINOGEN, M-PROTEIN, GROUP A STREPTOCOCCUS, BLOOD KEYWDS 2 CLOTTING EXPDTA ELECTRON MICROSCOPY AUTHOR B.M.READNOUR,S.K.TJIA-FLECK,F.J.CASTELLINO,N.R.MCCANN REVDAT 3 21-AUG-24 8TVL 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV HELIX ATOM REVDAT 2 13-DEC-23 8TVL 1 REMARK REVDAT 1 11-OCT-23 8TVL 0 JRNL AUTH B.M.READNOUR,S.K.TJIA-FLECK,N.R.MCCANN,Y.A.AYINUOLA, JRNL AUTH 2 V.A.PLOPLIS,F.J.CASTELLINO JRNL TITL PLASMINOGEN BINDING GROUP A STREPTOCOCCUS M-LIKE PROTEIN JRNL TITL 2 FROM AP53 BOUND TO HUMAN PLASMINOGEN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : RIGID BODY FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.800 REMARK 3 NUMBER OF PARTICLES : 212829 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8TVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276743. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : PLASMINOGEN BINDING GROUP A REMARK 245 STREPTOCOCCUS M-LIKE PROTEIN REMARK 245 FROM AP53 BOUND TO HUMAN REMARK 245 PLASMINOGEN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : PAM WAS BOUND TO THE SURFACE OF REMARK 245 A LENTIVIRUS REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 4054 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 34000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : 109000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASN A 1 REMARK 465 ARG A 2 REMARK 465 ALA A 3 REMARK 465 ASP A 4 REMARK 465 ASP A 5 REMARK 465 ALA A 6 REMARK 465 ARG A 7 REMARK 465 ASN A 8 REMARK 465 GLU A 9 REMARK 465 VAL A 10 REMARK 465 LEU A 11 REMARK 465 ARG A 12 REMARK 465 GLY A 13 REMARK 465 ASN A 14 REMARK 465 LEU A 15 REMARK 465 VAL A 16 REMARK 465 ARG A 17 REMARK 465 ALA A 18 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 OD1 ASP A 150 HZ2 LYS A 200 1.44 REMARK 500 OE1 GLN A 330 HE22 GLN A 340 1.52 REMARK 500 O LYS A 201 HZ3 LYS A 205 1.57 REMARK 500 OG SER A 182 HH21 ARG A 186 1.60 REMARK 500 OE2 GLU A 204 OG1 THR A 211 1.96 REMARK 500 NH1 ARG A 123 OE2 GLU A 136 2.08 REMARK 500 O LYS A 201 NZ LYS A 205 2.10 REMARK 500 O ILE A 223 OG SER A 227 2.15 REMARK 500 OE1 GLN A 330 NE2 GLN A 340 2.18 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 TRP A 21 101.24 -160.35 REMARK 500 ASN A 28 -104.70 -152.70 REMARK 500 LYS A 32 122.48 67.36 REMARK 500 ARG A 43 -30.82 -132.28 REMARK 500 GLU A 44 -68.43 74.47 REMARK 500 GLU A 46 65.10 62.11 REMARK 500 GLU A 47 -162.29 -78.34 REMARK 500 GLN A 50 49.83 -89.83 REMARK 500 LEU A 52 76.58 -100.18 REMARK 500 LYS A 53 -176.45 -69.82 REMARK 500 GLU A 57 -110.37 136.98 REMARK 500 LYS A 58 46.15 -140.42 REMARK 500 ALA A 61 23.66 85.26 REMARK 500 GLN A 66 62.79 65.30 REMARK 500 ARG A 67 18.68 -141.47 REMARK 500 LEU A 68 -159.08 -73.68 REMARK 500 GLU A 71 176.92 -59.92 REMARK 500 ARG A 72 41.89 -87.60 REMARK 500 HIS A 73 170.08 178.45 REMARK 500 ALA A 76 5.44 -68.79 REMARK 500 GLU A 77 81.14 -66.78 REMARK 500 GLU A 79 0.69 -66.98 REMARK 500 SER A 83 52.27 -91.18 REMARK 500 LYS A 91 -8.47 76.09 REMARK 500 GLU A 92 -100.62 168.13 REMARK 500 GLU A 94 37.09 73.02 REMARK 500 ARG A 95 -101.97 -166.02 REMARK 500 LYS A 101 -165.34 53.17 REMARK 500 GLN A 106 106.56 -164.85 REMARK 500 GLU A 107 44.71 35.45 REMARK 500 LEU A 109 77.85 -69.59 REMARK 500 ALA A 112 -11.26 75.74 REMARK 500 GLU A 118 43.38 -92.38 REMARK 500 LYS A 119 76.35 -68.85 REMARK 500 ALA A 121 47.93 -82.35 REMARK 500 GLU A 122 46.05 33.53 REMARK 500 LYS A 132 66.32 60.93 REMARK 500 LEU A 133 42.53 -109.33 REMARK 500 LYS A 137 -70.32 -114.41 REMARK 500 ARG A 148 -66.85 -90.17 REMARK 500 LYS A 163 -50.99 -122.73 REMARK 500 GLU A 171 -10.07 71.12 REMARK 500 LYS A 174 49.22 39.10 REMARK 500 ARG A 190 -52.59 -120.02 REMARK 500 ARG A 197 3.51 -63.64 REMARK 500 LYS A 200 -55.02 -121.35 REMARK 500 LYS A 201 -4.38 -55.14 REMARK 500 VAL A 203 0.87 -69.14 REMARK 500 LYS A 216 167.05 81.27 REMARK 500 GLU A 219 47.24 -90.70 REMARK 500 REMARK 500 THIS ENTRY HAS 85 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 50 GLY A 51 145.34 REMARK 500 GLU A 75 ALA A 76 145.61 REMARK 500 ARG A 197 GLU A 198 145.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42429 RELATED DB: EMDB DBREF 8TVL A 1 356 UNP P49054 PAM_STRPY 30 385 SEQADV 8TVL ARG A 123 UNP P49054 ALA 152 CONFLICT SEQRES 1 A 356 ASN ARG ALA ASP ASP ALA ARG ASN GLU VAL LEU ARG GLY SEQRES 2 A 356 ASN LEU VAL ARG ALA GLU LEU TRP TYR ARG GLN ILE GLN SEQRES 3 A 356 GLU ASN ASP GLN LEU LYS LEU GLU ASN LYS GLY LEU LYS SEQRES 4 A 356 THR ASP LEU ARG GLU LYS GLU GLU GLU LEU GLN GLY LEU SEQRES 5 A 356 LYS ASP ASP VAL GLU LYS LEU THR ALA ASP ALA GLU LEU SEQRES 6 A 356 GLN ARG LEU LYS ASN GLU ARG HIS GLU GLU ALA GLU LEU SEQRES 7 A 356 GLU ARG LEU LYS SER GLU ARG HIS ASP HIS ASP LYS LYS SEQRES 8 A 356 GLU ALA GLU ARG LYS ALA LEU GLU ASP LYS LEU ALA ASP SEQRES 9 A 356 LYS GLN GLU HIS LEU ASN GLY ALA LEU ARG TYR ILE ASN SEQRES 10 A 356 GLU LYS GLU ALA GLU ARG LYS GLU LYS GLU ALA GLU GLN SEQRES 11 A 356 LYS LYS LEU LYS GLU GLU LYS GLN ILE SER ASP ALA SER SEQRES 12 A 356 ARG GLN GLY LEU ARG ARG ASP LEU ASP ALA SER ARG GLU SEQRES 13 A 356 ALA LYS LYS GLN VAL GLU LYS ASP LEU ALA ASN LEU THR SEQRES 14 A 356 ALA GLU LEU ASP LYS VAL LYS GLU GLU LYS GLN ILE SER SEQRES 15 A 356 ASP ALA SER ARG GLN GLY LEU ARG ARG ASP LEU ASP ALA SEQRES 16 A 356 SER ARG GLU ALA LYS LYS GLN VAL GLU LYS GLY LEU ALA SEQRES 17 A 356 ASN LEU THR ALA GLU LEU ASP LYS VAL LYS GLU GLU LYS SEQRES 18 A 356 GLN ILE SER ASP ALA SER ARG GLN GLY LEU ARG ARG ASP SEQRES 19 A 356 LEU ASP ALA SER ARG GLU ALA LYS LYS GLN VAL GLU LYS SEQRES 20 A 356 ALA LEU GLU GLU ALA ASN SER LYS LEU ALA ALA LEU GLU SEQRES 21 A 356 LYS LEU ASN LYS GLU LEU GLU GLU SER LYS LYS LEU THR SEQRES 22 A 356 GLU LYS GLU LYS ALA GLU LEU GLN ALA LYS LEU GLU ALA SEQRES 23 A 356 GLU ALA LYS ALA LEU LYS GLU GLN LEU ALA LYS GLN ALA SEQRES 24 A 356 GLU GLU LEU ALA LYS LEU ARG ALA GLU LYS ALA SER ASP SEQRES 25 A 356 SER GLN THR PRO ASP ALA LYS PRO GLY ASN LYS ALA VAL SEQRES 26 A 356 PRO GLY LYS GLY GLN ALA PRO GLN ALA GLY THR LYS PRO SEQRES 27 A 356 ASN GLN ASN LYS ALA PRO MET LYS GLU THR LYS ARG GLN SEQRES 28 A 356 LEU PRO SER THR GLY HELIX 1 AA1 LEU A 78 LYS A 82 5 5 HELIX 2 AA2 LYS A 137 LEU A 147 1 11 HELIX 3 AA3 LYS A 163 ASN A 167 5 5 HELIX 4 AA4 GLU A 177 SER A 182 1 6 HELIX 5 AA5 SER A 182 GLN A 187 1 6 HELIX 6 AA6 ARG A 190 SER A 196 1 7 HELIX 7 AA7 ARG A 197 GLN A 202 1 6 HELIX 8 AA8 LYS A 221 ASP A 234 1 14 HELIX 9 AA9 ASP A 236 ALA A 241 1 6 HELIX 10 AB1 ASN A 263 LEU A 272 1 10 HELIX 11 AB2 LEU A 280 LEU A 291 1 12 HELIX 12 AB3 LYS A 292 ALA A 299 1 8 HELIX 13 AB4 ALA A 318 LYS A 323 1 6 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 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 TER 5480 GLY A 356 MASTER 228 0 0 13 0 0 0 6 2706 1 0 28 END