PDB Short entry for 4JFN HEADER METAL BINDING PROTEIN 28-FEB-13 4JFN TITLE CRYSTAL STRUCTURE OF THE N-TERMINAL, GROWTH FACTOR-LIKE DOMAIN OF THE TITLE 2 AMYLOID PRECURSOR PROTEIN BOUND TO COPPER COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID BETA A4 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GROWTH FACTOR-LIKE DOMAIN (GFLD), UNP RESIDUES 23-185; COMPND 5 SYNONYM: ABPP, APPI, APP, ALZHEIMER DISEASE AMYLOID PROTEIN, CEREBRAL COMPND 6 VASCULAR AMYLOID PEPTIDE, CVAP, PREA4, PROTEASE NEXIN-II, PN-II, N- COMPND 7 APP, SOLUBLE APP-ALPHA, S-APP-ALPHA, SOLUBLE APP-BETA, S-APP-BETA, COMPND 8 C99, BETA-AMYLOID PROTEIN 42, BETA-APP42, BETA-AMYLOID PROTEIN 40, COMPND 9 BETA-APP40, C83, P3(42), P3(40), C80, GAMMA-SECRETASE C-TERMINAL COMPND 10 FRAGMENT 59, AMYLOID INTRACELLULAR DOMAIN 59, AICD-59, AID(59), COMPND 11 GAMMA-CTF(59), GAMMA-SECRETASE C-TERMINAL FRAGMENT 57, AMYLOID COMPND 12 INTRACELLULAR DOMAIN 57, AICD-57, AID(57), GAMMA-CTF(57), GAMMA- COMPND 13 SECRETASE C-TERMINAL FRAGMENT 50, AMYLOID INTRACELLULAR DOMAIN 50, COMPND 14 AICD-50, AID(50), GAMMA-CTF(50), C31; COMPND 15 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: APP, A4, AD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALZHEIMER'S DISEASE, GFLD, APP, GROWTH FACTOR-LIKE DOMAIN, COPPER KEYWDS 2 BINDING, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.WILD,F.BAUMKOTTER,S.KINS REVDAT 3 08-NOV-23 4JFN 1 REMARK LINK REVDAT 2 03-SEP-14 4JFN 1 JRNL REVDAT 1 23-JUL-14 4JFN 0 JRNL AUTH F.BAUMKOTTER,N.SCHMIDT,C.VARGAS,S.SCHILLING,R.WEBER, JRNL AUTH 2 K.WAGNER,S.FIEDLER,W.KLUG,J.RADZIMANOWSKI,S.NICKOLAUS, JRNL AUTH 3 S.KELLER,S.EGGERT,K.WILD,S.KINS JRNL TITL AMYLOID PRECURSOR PROTEIN DIMERIZATION AND SYNAPTOGENIC JRNL TITL 2 FUNCTION DEPEND ON COPPER BINDING TO THE GROWTH FACTOR-LIKE JRNL TITL 3 DOMAIN JRNL REF J.NEUROSCI. V. 34 11159 2014 JRNL REFN ISSN 0270-6474 JRNL PMID 25122912 JRNL DOI 10.1523/JNEUROSCI.0180-14.2014 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 11659 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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 30.2801 - 2.7774 0.99 2887 155 0.1732 0.1933 REMARK 3 2 2.7774 - 2.2047 1.00 2767 132 0.1958 0.3018 REMARK 3 3 2.2047 - 1.9261 1.00 2733 139 0.1678 0.2620 REMARK 3 4 1.9261 - 1.7500 1.00 2718 128 0.2179 0.2906 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.41 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 : 0.007 857 REMARK 3 ANGLE : 1.156 1166 REMARK 3 CHIRALITY : 0.084 124 REMARK 3 PLANARITY : 0.004 154 REMARK 3 DIHEDRAL : 14.018 325 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JFN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000077985. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11659 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 30.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1MWP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 17.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% (W/V) PEG 3350, 0.1 M HEPES, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 17.02500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.08000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.53500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.08000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.02500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.53500 REMARK 290 SMTRY3 4 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 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 SER A 124 REMARK 465 ASP A 125 REMARK 465 ALA A 126 REMARK 465 LEU A 127 REMARK 465 LEU A 128 REMARK 465 VAL A 129 REMARK 465 PRO A 130 REMARK 465 ASP A 131 REMARK 465 LYS A 132 REMARK 465 CYS A 133 REMARK 465 LYS A 134 REMARK 465 PHE A 135 REMARK 465 LEU A 136 REMARK 465 HIS A 137 REMARK 465 GLN A 138 REMARK 465 GLU A 139 REMARK 465 ARG A 140 REMARK 465 MET A 141 REMARK 465 ASP A 142 REMARK 465 VAL A 143 REMARK 465 CYS A 144 REMARK 465 GLU A 145 REMARK 465 THR A 146 REMARK 465 HIS A 147 REMARK 465 LEU A 148 REMARK 465 HIS A 149 REMARK 465 TRP A 150 REMARK 465 HIS A 151 REMARK 465 THR A 152 REMARK 465 VAL A 153 REMARK 465 ALA A 154 REMARK 465 LYS A 155 REMARK 465 GLU A 156 REMARK 465 THR A 157 REMARK 465 CYS A 158 REMARK 465 SER A 159 REMARK 465 GLU A 160 REMARK 465 LYS A 161 REMARK 465 SER A 162 REMARK 465 THR A 163 REMARK 465 ASN A 164 REMARK 465 LEU A 165 REMARK 465 HIS A 166 REMARK 465 ASP A 167 REMARK 465 TYR A 168 REMARK 465 GLY A 169 REMARK 465 MET A 170 REMARK 465 LEU A 171 REMARK 465 LEU A 172 REMARK 465 PRO A 173 REMARK 465 CYS A 174 REMARK 465 GLY A 175 REMARK 465 ILE A 176 REMARK 465 ASP A 177 REMARK 465 LYS A 178 REMARK 465 PHE A 179 REMARK 465 ARG A 180 REMARK 465 GLY A 181 REMARK 465 VAL A 182 REMARK 465 GLU A 183 REMARK 465 PHE A 184 REMARK 465 VAL A 185 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 THR A 61 -164.11 -110.88 REMARK 500 ARG A 102 38.60 -151.69 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 CU A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 108 NE2 REMARK 620 2 HIS A 110 NE2 99.2 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 202 DBREF 4JFN A 23 185 UNP P05067 A4_HUMAN 23 185 SEQRES 1 A 163 ASP GLY ASN ALA GLY LEU LEU ALA GLU PRO GLN ILE ALA SEQRES 2 A 163 MET PHE CYS GLY ARG LEU ASN MET HIS MET ASN VAL GLN SEQRES 3 A 163 ASN GLY LYS TRP ASP SER ASP PRO SER GLY THR LYS THR SEQRES 4 A 163 CYS ILE ASP THR LYS GLU GLY ILE LEU GLN TYR CYS GLN SEQRES 5 A 163 GLU VAL TYR PRO GLU LEU GLN ILE THR ASN VAL VAL GLU SEQRES 6 A 163 ALA ASN GLN PRO VAL THR ILE GLN ASN TRP CYS LYS ARG SEQRES 7 A 163 GLY ARG LYS GLN CYS LYS THR HIS PRO HIS PHE VAL ILE SEQRES 8 A 163 PRO TYR ARG CYS LEU VAL GLY GLU PHE VAL SER ASP ALA SEQRES 9 A 163 LEU LEU VAL PRO ASP LYS CYS LYS PHE LEU HIS GLN GLU SEQRES 10 A 163 ARG MET ASP VAL CYS GLU THR HIS LEU HIS TRP HIS THR SEQRES 11 A 163 VAL ALA LYS GLU THR CYS SER GLU LYS SER THR ASN LEU SEQRES 12 A 163 HIS ASP TYR GLY MET LEU LEU PRO CYS GLY ILE ASP LYS SEQRES 13 A 163 PHE ARG GLY VAL GLU PHE VAL HET CU A 201 1 HET GOL A 202 6 HETNAM CU COPPER (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CU CU 2+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *52(H2 O) HELIX 1 1 THR A 65 TYR A 77 1 13 SHEET 1 A 5 TRP A 52 SER A 54 0 SHEET 2 A 5 MET A 43 MET A 45 -1 N HIS A 44 O ASP A 53 SHEET 3 A 5 GLN A 33 ALA A 35 -1 N ALA A 35 O MET A 43 SHEET 4 A 5 TYR A 115 VAL A 119 -1 O TYR A 115 N ILE A 34 SHEET 5 A 5 ILE A 82 GLU A 87 -1 N VAL A 86 O ARG A 116 SHEET 1 B 2 VAL A 92 ILE A 94 0 SHEET 2 B 2 HIS A 110 VAL A 112 -1 O VAL A 112 N VAL A 92 SSBOND 1 CYS A 38 CYS A 62 1555 1555 2.04 SSBOND 2 CYS A 73 CYS A 117 1555 1555 2.06 LINK NE2 HIS A 108 CU CU A 201 1555 1555 2.03 LINK NE2 HIS A 110 CU CU A 201 1555 1555 1.95 SITE 1 AC1 4 ASP A 23 ARG A 40 HIS A 108 HIS A 110 SITE 1 AC2 9 HIS A 44 MET A 45 ASN A 46 VAL A 47 SITE 2 AC2 9 ASP A 53 VAL A 76 TYR A 77 GLN A 90 SITE 3 AC2 9 HOH A 327 CRYST1 34.050 49.070 66.160 90.00 90.00 90.00 P 21 21 21 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 0.029369 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015115 0.00000