PDB Short entry for 5TPT HEADER PROTEIN FIBRIL 21-OCT-16 5TPT TITLE THE CRYSTAL STRUCTURE OF AMYLOID PRECURSOR-LIKE PROTEIN 2 (APLP2) E2 TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-LIKE PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 373-569; COMPND 5 SYNONYM: APLP-2,APPH,AMYLOID PROTEIN HOMOLOG,CDEI BOX-BINDING COMPND 6 PROTEIN,CDEBP; COMPND 7 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: APLP2, APPL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS AMYLOID PRECURSOR PROTEIN FAMILY, ALZHEIMER'S DISEASE, PROTEIN FIBRIL EXPDTA X-RAY DIFFRACTION AUTHOR L.C.ROISMAN,R.CAPPAI REVDAT 3 17-JAN-24 5TPT 1 REMARK REVDAT 2 29-MAY-19 5TPT 1 AUTHOR JRNL REVDAT 1 06-JUN-18 5TPT 0 JRNL AUTH L.C.ROISMAN,S.HAN,M.J.CHUEI,A.R.CONNOR,R.CAPPAI JRNL TITL THE CRYSTAL STRUCTURE OF AMYLOID PRECURSOR-LIKE PROTEIN 2 E2 JRNL TITL 2 DOMAIN COMPLETES THE AMYLOID PRECURSOR PROTEIN FAMILY. JRNL REF FASEB J. V. 33 5076 2019 JRNL REFN ESSN 1530-6860 JRNL PMID 30608876 JRNL DOI 10.1096/FJ.201802315R REMARK 2 REMARK 2 RESOLUTION. 2.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 14677 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.5340 - 5.2138 1.00 1346 150 0.2137 0.2494 REMARK 3 2 5.2138 - 4.1401 1.00 1344 149 0.1878 0.2147 REMARK 3 3 4.1401 - 3.6172 1.00 1297 144 0.1940 0.2212 REMARK 3 4 3.6172 - 3.2867 1.00 1319 147 0.2011 0.2904 REMARK 3 5 3.2867 - 3.0512 1.00 1336 148 0.2334 0.2809 REMARK 3 6 3.0512 - 2.8714 1.00 1320 148 0.2215 0.2881 REMARK 3 7 2.8714 - 2.7277 0.99 1308 145 0.2374 0.3083 REMARK 3 8 2.7277 - 2.6089 0.99 1322 146 0.2499 0.2956 REMARK 3 9 2.6089 - 2.5085 0.99 1325 147 0.2452 0.2849 REMARK 3 10 2.5085 - 2.4220 0.99 1292 144 0.2413 0.2781 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.74 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 3219 REMARK 3 ANGLE : 0.717 4326 REMARK 3 CHIRALITY : 0.030 467 REMARK 3 PLANARITY : 0.004 575 REMARK 3 DIHEDRAL : 14.355 1291 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 1766 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5TPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224599. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 REMARK 200 MONOCHROMATOR : SILICON DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14709 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.420 REMARK 200 RESOLUTION RANGE LOW (A) : 37.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.84100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3UMI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M PHOSPHATE-CITRATE, 40% PEG400, REMARK 280 PH 4.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298.15K 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 75.05900 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP B 373 REMARK 465 VAL B 374 REMARK 465 ASP B 375 REMARK 465 VAL B 376 REMARK 465 TYR B 377 REMARK 465 PHE B 378 REMARK 465 GLU B 379 REMARK 465 THR B 380 REMARK 465 SER B 381 REMARK 465 ALA B 382 REMARK 465 ASP B 383 REMARK 465 ASP B 384 REMARK 465 ASN B 385 REMARK 465 GLU B 386 REMARK 465 GLN B 568 REMARK 465 ARG B 569 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 OE1 GLU B 413 O HOH B 601 2.16 REMARK 500 NH2 ARG A 504 O HOH A 601 2.16 REMARK 500 O HOH A 606 O HOH A 638 2.16 REMARK 500 OG SER A 447 O ALA B 440 2.17 REMARK 500 O ALA A 440 OG SER B 447 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 5TPT A 373 569 UNP Q06481 APLP2_HUMAN 373 569 DBREF 5TPT B 373 569 UNP Q06481 APLP2_HUMAN 373 569 SEQRES 1 A 197 ASP VAL ASP VAL TYR PHE GLU THR SER ALA ASP ASP ASN SEQRES 2 A 197 GLU HIS ALA ARG PHE GLN LYS ALA LYS GLU GLN LEU GLU SEQRES 3 A 197 ILE ARG HIS ARG ASN ARG MET ASP ARG VAL LYS LYS GLU SEQRES 4 A 197 TRP GLU GLU ALA GLU LEU GLN ALA LYS ASN LEU PRO LYS SEQRES 5 A 197 ALA GLU ARG GLN THR LEU ILE GLN HIS PHE GLN ALA MET SEQRES 6 A 197 VAL LYS ALA LEU GLU LYS GLU ALA ALA SER GLU LYS GLN SEQRES 7 A 197 GLN LEU VAL GLU THR HIS LEU ALA ARG VAL GLU ALA MET SEQRES 8 A 197 LEU ASN ASP ARG ARG ARG MET ALA LEU GLU ASN TYR LEU SEQRES 9 A 197 ALA ALA LEU GLN SER ASP PRO PRO ARG PRO HIS ARG ILE SEQRES 10 A 197 LEU GLN ALA LEU ARG ARG TYR VAL ARG ALA GLU ASN LYS SEQRES 11 A 197 ASP ARG LEU HIS THR ILE ARG HIS TYR GLN HIS VAL LEU SEQRES 12 A 197 ALA VAL ASP PRO GLU LYS ALA ALA GLN MET LYS SER GLN SEQRES 13 A 197 VAL MET THR HIS LEU HIS VAL ILE GLU GLU ARG ARG ASN SEQRES 14 A 197 GLN SER LEU SER LEU LEU TYR LYS VAL PRO TYR VAL ALA SEQRES 15 A 197 GLN GLU ILE GLN GLU GLU ILE ASP GLU LEU LEU GLN GLU SEQRES 16 A 197 GLN ARG SEQRES 1 B 197 ASP VAL ASP VAL TYR PHE GLU THR SER ALA ASP ASP ASN SEQRES 2 B 197 GLU HIS ALA ARG PHE GLN LYS ALA LYS GLU GLN LEU GLU SEQRES 3 B 197 ILE ARG HIS ARG ASN ARG MET ASP ARG VAL LYS LYS GLU SEQRES 4 B 197 TRP GLU GLU ALA GLU LEU GLN ALA LYS ASN LEU PRO LYS SEQRES 5 B 197 ALA GLU ARG GLN THR LEU ILE GLN HIS PHE GLN ALA MET SEQRES 6 B 197 VAL LYS ALA LEU GLU LYS GLU ALA ALA SER GLU LYS GLN SEQRES 7 B 197 GLN LEU VAL GLU THR HIS LEU ALA ARG VAL GLU ALA MET SEQRES 8 B 197 LEU ASN ASP ARG ARG ARG MET ALA LEU GLU ASN TYR LEU SEQRES 9 B 197 ALA ALA LEU GLN SER ASP PRO PRO ARG PRO HIS ARG ILE SEQRES 10 B 197 LEU GLN ALA LEU ARG ARG TYR VAL ARG ALA GLU ASN LYS SEQRES 11 B 197 ASP ARG LEU HIS THR ILE ARG HIS TYR GLN HIS VAL LEU SEQRES 12 B 197 ALA VAL ASP PRO GLU LYS ALA ALA GLN MET LYS SER GLN SEQRES 13 B 197 VAL MET THR HIS LEU HIS VAL ILE GLU GLU ARG ARG ASN SEQRES 14 B 197 GLN SER LEU SER LEU LEU TYR LYS VAL PRO TYR VAL ALA SEQRES 15 B 197 GLN GLU ILE GLN GLU GLU ILE ASP GLU LEU LEU GLN GLU SEQRES 16 B 197 GLN ARG FORMUL 3 HOH *75(H2 O) HELIX 1 AA1 ASP A 373 PHE A 378 1 6 HELIX 2 AA2 ASN A 385 GLN A 418 1 34 HELIX 3 AA3 PRO A 423 SER A 481 1 59 HELIX 4 AA4 ARG A 485 ASP A 518 1 34 HELIX 5 AA5 ASP A 518 LEU A 546 1 29 HELIX 6 AA6 LEU A 547 LYS A 549 5 3 HELIX 7 AA7 VAL A 550 ILE A 557 1 8 HELIX 8 AA8 ILE A 557 GLU A 567 1 11 HELIX 9 AA9 ALA B 388 GLN B 418 1 31 HELIX 10 AB1 PRO B 423 GLN B 480 1 58 HELIX 11 AB2 ARG B 485 ASP B 518 1 34 HELIX 12 AB3 ASP B 518 LEU B 546 1 29 HELIX 13 AB4 VAL B 550 ILE B 557 1 8 HELIX 14 AB5 ILE B 557 GLN B 566 1 10 CISPEP 1 ASP A 482 PRO A 483 0 -1.27 CISPEP 2 ASP B 482 PRO B 483 0 -2.31 CRYST1 35.749 150.118 39.107 90.00 109.69 90.00 P 1 21 1 4 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 0.027973 0.000000 0.010009 0.00000 SCALE2 0.000000 0.006661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027159 0.00000