HEADER HYDROLASE 04-AUG-17 5ONQ TITLE ALZHEIMER'S AMYLOID-BETA PEPTIDE FRAGMENT 29-40 IN COMPLEX WITH CD- TITLE 2 SUBSTITUTED THERMOLYSIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMOLYSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEUTRAL PROTEASE; COMPND 5 EC: 3.4.24.27; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: AMYLOID-BETA A4 PROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: ABPP,APPI,APP,ALZHEIMER DISEASE AMYLOID PROTEIN,AMYLOID COMPND 10 PRECURSOR PROTEIN,AMYLOID-BETA PRECURSOR PROTEIN,CEREBRAL VASCULAR COMPND 11 AMYLOID PEPTIDE,CVAP,PREA4,PROTEASE NEXIN-II,PN-II; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: BACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606 KEYWDS PEPTIDASE, PROTEIN-PEPTIDE COMPLEX, AMYLOID-BETA PEPTIDE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.P.LEITE,L.GALES REVDAT 3 17-JAN-24 5ONQ 1 LINK REVDAT 2 06-FEB-19 5ONQ 1 JRNL REVDAT 1 29-AUG-18 5ONQ 0 JRNL AUTH J.P.LEITE,L.GALES JRNL TITL ALZHEIMER'S A BETA1-40PEPTIDE DEGRADATION BY THERMOLYSIN: JRNL TITL 2 EVIDENCE OF INHIBITION BY A C-TERMINAL A BETA PRODUCT. JRNL REF FEBS LETT. V. 593 128 2019 JRNL REFN ISSN 1873-3468 JRNL PMID 30403288 JRNL DOI 10.1002/1873-3468.13285 REMARK 2 REMARK 2 RESOLUTION. 1.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 111610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.172 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 5700 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 44.0007 - 3.6348 0.99 3872 208 0.1615 0.1632 REMARK 3 2 3.6348 - 2.8852 1.00 3687 210 0.1581 0.1774 REMARK 3 3 2.8852 - 2.5206 0.99 3622 197 0.1612 0.1590 REMARK 3 4 2.5206 - 2.2901 1.00 3623 187 0.1555 0.1558 REMARK 3 5 2.2901 - 2.1260 1.00 3586 181 0.1450 0.1531 REMARK 3 6 2.1260 - 2.0006 1.00 3601 192 0.1420 0.1415 REMARK 3 7 2.0006 - 1.9004 0.99 3542 189 0.1426 0.1562 REMARK 3 8 1.9004 - 1.8177 1.00 3562 181 0.1429 0.1601 REMARK 3 9 1.8177 - 1.7477 1.00 3604 168 0.1403 0.1350 REMARK 3 10 1.7477 - 1.6874 1.00 3556 177 0.1405 0.1566 REMARK 3 11 1.6874 - 1.6347 1.00 3542 185 0.1393 0.1599 REMARK 3 12 1.6347 - 1.5879 1.00 3534 193 0.1388 0.1417 REMARK 3 13 1.5879 - 1.5461 1.00 3509 214 0.1435 0.1759 REMARK 3 14 1.5461 - 1.5084 0.99 3495 195 0.1542 0.1792 REMARK 3 15 1.5084 - 1.4741 1.00 3544 186 0.1601 0.1662 REMARK 3 16 1.4741 - 1.4427 1.00 3496 195 0.1794 0.2277 REMARK 3 17 1.4427 - 1.4139 1.00 3507 189 0.1712 0.1749 REMARK 3 18 1.4139 - 1.3872 1.00 3530 195 0.1634 0.1743 REMARK 3 19 1.3872 - 1.3624 0.98 3413 194 0.1985 0.2010 REMARK 3 20 1.3624 - 1.3393 0.99 3484 210 0.1851 0.1995 REMARK 3 21 1.3393 - 1.3177 1.00 3476 204 0.1740 0.1782 REMARK 3 22 1.3177 - 1.2974 1.00 3511 164 0.1963 0.2199 REMARK 3 23 1.2974 - 1.2784 1.00 3498 194 0.2029 0.2302 REMARK 3 24 1.2784 - 1.2603 0.99 3494 177 0.2368 0.2490 REMARK 3 25 1.2603 - 1.2433 0.99 3449 181 0.2420 0.2236 REMARK 3 26 1.2433 - 1.2272 0.99 3453 209 0.2260 0.2457 REMARK 3 27 1.2272 - 1.2118 0.99 3439 177 0.2595 0.2679 REMARK 3 28 1.2118 - 1.1972 0.99 3466 185 0.2215 0.2614 REMARK 3 29 1.1972 - 1.1833 0.98 3429 174 0.2315 0.2126 REMARK 3 30 1.1833 - 1.1700 0.96 3386 189 0.2560 0.2495 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.64 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 : 0.005 2577 REMARK 3 ANGLE : 0.822 3518 REMARK 3 CHIRALITY : 0.083 376 REMARK 3 PLANARITY : 0.005 464 REMARK 3 DIHEDRAL : 4.820 1866 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.5400 30.8993 -2.4989 REMARK 3 T TENSOR REMARK 3 T11: 0.0642 T22: 0.0824 REMARK 3 T33: 0.0778 T12: 0.0075 REMARK 3 T13: 0.0190 T23: -0.0017 REMARK 3 L TENSOR REMARK 3 L11: 1.1050 L22: 0.3307 REMARK 3 L33: 0.4392 L12: 0.1669 REMARK 3 L13: 0.4655 L23: 0.0671 REMARK 3 S TENSOR REMARK 3 S11: 0.0184 S12: -0.0164 S13: -0.0182 REMARK 3 S21: 0.0291 S22: -0.0235 S23: 0.0538 REMARK 3 S31: 0.0227 S32: -0.0447 S33: 0.0033 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 5ONQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200005458. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97264 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BE CRL LENSES FOR VERTICAL REMARK 200 FOCUSING AND RH/PT/SI COATED REMARK 200 ELLIPITCAL MIRROR FOR HORIZONTAL REMARK 200 FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 111781 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.170 REMARK 200 RESOLUTION RANGE LOW (A) : 46.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.10 REMARK 200 R MERGE FOR SHELL (I) : 0.86700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDBID 1KEI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM MES: 45% DMSO: 0.7-0.9 M NACL: 0 REMARK 280 -0.4 M CDCL2: RESERVOIR SOLUTION CONTAINING 30-40% AMMONIUM REMARK 280 SULPHATE, PH 6.0, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.18600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.37200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.77900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 107.96500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 21.59300 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.18600 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 86.37200 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 107.96500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 64.77900 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 21.59300 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: 1440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 769 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 798 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 872 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 158 CD OE1 NE2 REMARK 470 GLN A 225 CG CD OE1 NE2 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 O HOH A 733 O HOH A 790 1.96 REMARK 500 O HOH A 744 O HOH A 797 2.11 REMARK 500 O HOH A 578 O HOH A 796 2.11 REMARK 500 O HOH A 743 O HOH A 796 2.14 REMARK 500 NH2 ARG A 11 O HOH A 501 2.15 REMARK 500 O HOH A 683 O HOH A 878 2.18 REMARK 500 O HOH A 712 O HOH A 743 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 796 O HOH A 796 7555 2.17 REMARK 500 O HOH A 773 O HOH A 819 7555 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 THR A 26 -58.89 68.80 REMARK 500 SER A 92 -172.77 59.87 REMARK 500 SER A 107 -163.66 59.57 REMARK 500 ASN A 111 56.63 -93.44 REMARK 500 SER A 118 -31.63 -132.67 REMARK 500 THR A 152 -100.96 -125.15 REMARK 500 ASN A 159 -141.73 55.46 REMARK 500 THR A 194 77.32 42.24 REMARK 500 ILE A 232 -60.24 -99.34 REMARK 500 ALA B 30 -46.44 -162.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 891 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 892 DISTANCE = 6.03 ANGSTROMS 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 CD A 405 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 57 OD1 REMARK 620 2 ASP A 57 OD2 51.0 REMARK 620 3 ASP A 59 OD1 118.2 67.6 REMARK 620 4 GLN A 61 O 91.8 86.3 91.0 REMARK 620 5 HOH A 538 O 160.0 147.7 80.1 96.0 REMARK 620 6 HOH A 586 O 85.5 134.6 155.6 82.3 77.4 REMARK 620 7 HOH A 779 O 86.9 89.4 85.7 175.3 86.7 102.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 404 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 138 OD2 REMARK 620 2 GLU A 177 OE2 81.9 REMARK 620 3 ASP A 185 OD1 160.3 117.6 REMARK 620 4 GLU A 187 O 85.1 148.0 79.2 REMARK 620 5 GLU A 190 OE1 84.5 128.3 81.0 78.9 REMARK 620 6 GLU A 190 OE2 96.3 81.2 84.9 129.4 51.2 REMARK 620 7 HOH A 574 O 100.7 80.1 86.2 73.9 151.6 152.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 402 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 142 NE2 REMARK 620 2 GLU A 143 OE2 75.2 REMARK 620 3 HIS A 146 NE2 96.5 93.0 REMARK 620 4 GLU A 166 OE1 114.3 169.7 90.0 REMARK 620 5 ALA B 30 O 101.7 84.0 160.1 89.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 403 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 177 OE1 REMARK 620 2 ASN A 183 O 90.0 REMARK 620 3 ASP A 185 OD2 92.4 87.8 REMARK 620 4 GLU A 190 OE2 89.7 172.2 84.4 REMARK 620 5 HOH A 528 O 174.6 89.2 92.9 91.9 REMARK 620 6 HOH A 533 O 86.9 93.5 178.5 94.2 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 193 O REMARK 620 2 THR A 194 O 76.7 REMARK 620 3 THR A 194 OG1 76.5 71.6 REMARK 620 4 ILE A 197 O 154.3 79.2 104.2 REMARK 620 5 ASP A 200 OD1 121.7 134.6 73.5 82.1 REMARK 620 6 HOH A 630 O 83.4 150.9 124.1 115.0 74.2 REMARK 620 7 HOH A 726 O 89.4 83.2 153.3 78.9 132.7 75.5 REMARK 620 N 1 2 3 4 5 6 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CD A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ONP RELATED DB: PDB DBREF 5ONQ A 1 316 UNP P43133 THER_GEOSE 236 551 DBREF 5ONQ B 29 33 PDB 5ONQ 5ONQ 29 33 SEQRES 1 A 316 ILE THR GLY THR SER THR VAL GLY VAL GLY ARG GLY VAL SEQRES 2 A 316 LEU GLY ASP GLN LYS ASN ILE ASN THR THR TYR SER THR SEQRES 3 A 316 TYR TYR TYR LEU GLN ASP ASN THR ARG GLY ASN GLY ILE SEQRES 4 A 316 PHE THR TYR ASP ALA LYS TYR ARG THR THR LEU PRO GLY SEQRES 5 A 316 SER LEU TRP ALA ASP ALA ASP ASN GLN PHE PHE ALA SER SEQRES 6 A 316 TYR ASP ALA PRO ALA VAL ASP ALA HIS TYR TYR ALA GLY SEQRES 7 A 316 VAL THR TYR ASP TYR TYR LYS ASN VAL HIS ASN ARG LEU SEQRES 8 A 316 SER TYR ASP GLY ASN ASN ALA ALA ILE ARG SER SER VAL SEQRES 9 A 316 HIS TYR SER GLN GLY TYR ASN ASN ALA PHE TRP ASN GLY SEQRES 10 A 316 SER GLN MET VAL TYR GLY ASP GLY ASP GLY GLN THR PHE SEQRES 11 A 316 ILE PRO LEU SER GLY GLY ILE ASP VAL VAL ALA HIS GLU SEQRES 12 A 316 LEU THR HIS ALA VAL THR ASP TYR THR ALA GLY LEU ILE SEQRES 13 A 316 TYR GLN ASN GLU SER GLY ALA ILE ASN GLU ALA ILE SER SEQRES 14 A 316 ASP ILE PHE GLY THR LEU VAL GLU PHE TYR ALA ASN LYS SEQRES 15 A 316 ASN PRO ASP TRP GLU ILE GLY GLU ASP VAL TYR THR PRO SEQRES 16 A 316 GLY ILE SER GLY ASP SER LEU ARG SER MET SER ASP PRO SEQRES 17 A 316 ALA LYS TYR GLY ASP PRO ASP HIS TYR SER LYS ARG TYR SEQRES 18 A 316 THR GLY THR GLN ASP ASN GLY GLY VAL HIS ILE ASN SER SEQRES 19 A 316 GLY ILE ILE ASN LYS ALA ALA TYR LEU ILE SER GLN GLY SEQRES 20 A 316 GLY THR HIS TYR GLY VAL SER VAL VAL GLY ILE GLY ARG SEQRES 21 A 316 ASP LYS LEU GLY LYS ILE PHE TYR ARG ALA LEU THR GLN SEQRES 22 A 316 TYR LEU THR PRO THR SER ASN PHE SER GLN LEU ARG ALA SEQRES 23 A 316 ALA ALA VAL GLN SER ALA THR ASP LEU TYR GLY SER THR SEQRES 24 A 316 SER GLN GLU VAL ALA SER VAL LYS GLN ALA PHE ASP ALA SEQRES 25 A 316 VAL GLY VAL LYS SEQRES 1 B 5 GLY ALA ILE ILE GLY HET CA A 401 1 HET CD A 402 1 HET CD A 403 1 HET CD A 404 1 HET CD A 405 1 HET DMS A 406 4 HETNAM CA CALCIUM ION HETNAM CD CADMIUM ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 3 CA CA 2+ FORMUL 4 CD 4(CD 2+) FORMUL 8 DMS C2 H6 O S FORMUL 9 HOH *393(H2 O) HELIX 1 AA1 ALA A 64 TYR A 66 5 3 HELIX 2 AA2 ASP A 67 ASN A 89 1 23 HELIX 3 AA3 PRO A 132 GLY A 135 5 4 HELIX 4 AA4 GLY A 136 THR A 152 1 17 HELIX 5 AA5 GLN A 158 ASN A 181 1 24 HELIX 6 AA6 ASP A 207 GLY A 212 5 6 HELIX 7 AA7 HIS A 216 ARG A 220 5 5 HELIX 8 AA8 THR A 224 VAL A 230 1 7 HELIX 9 AA9 ASN A 233 GLY A 247 1 15 HELIX 10 AB1 GLY A 259 TYR A 274 1 16 HELIX 11 AB2 ASN A 280 GLY A 297 1 18 HELIX 12 AB3 SER A 300 VAL A 313 1 14 SHEET 1 AA1 5 ALA A 56 ASP A 57 0 SHEET 2 AA1 5 TYR A 28 TYR A 29 -1 N TYR A 28 O ASP A 57 SHEET 3 AA1 5 GLN A 17 TYR A 24 -1 N THR A 23 O TYR A 29 SHEET 4 AA1 5 THR A 4 ARG A 11 -1 N GLY A 8 O ILE A 20 SHEET 5 AA1 5 GLN A 61 PHE A 62 1 O PHE A 62 N VAL A 9 SHEET 1 AA2 3 GLN A 31 ASP A 32 0 SHEET 2 AA2 3 ILE A 39 ASP A 43 -1 O ILE A 39 N ASP A 32 SHEET 3 AA2 3 SER A 53 LEU A 54 -1 O SER A 53 N ASP A 43 SHEET 1 AA3 5 GLN A 31 ASP A 32 0 SHEET 2 AA3 5 ILE A 39 ASP A 43 -1 O ILE A 39 N ASP A 32 SHEET 3 AA3 5 ILE A 100 TYR A 106 1 O SER A 102 N TYR A 42 SHEET 4 AA3 5 MET A 120 GLY A 123 1 O MET A 120 N ARG A 101 SHEET 5 AA3 5 ALA A 113 TRP A 115 -1 N PHE A 114 O VAL A 121 SHEET 1 AA4 2 GLU A 187 ILE A 188 0 SHEET 2 AA4 2 ARG A 203 SER A 204 -1 O ARG A 203 N ILE A 188 SHEET 1 AA5 2 GLY A 248 HIS A 250 0 SHEET 2 AA5 2 VAL A 253 VAL A 255 -1 O VAL A 255 N GLY A 248 LINK OD1 ASP A 57 CD CD A 405 1555 1555 2.34 LINK OD2 ASP A 57 CD CD A 405 1555 1555 2.69 LINK OD1 ASP A 59 CD CD A 405 1555 1555 2.38 LINK O GLN A 61 CD CD A 405 1555 1555 2.27 LINK OD2 ASP A 138 CD CD A 404 1555 1555 2.38 LINK NE2 HIS A 142 CD CD A 402 1555 1555 2.31 LINK OE2 GLU A 143 CD CD A 402 1555 1555 2.61 LINK NE2 HIS A 146 CD CD A 402 1555 1555 2.33 LINK OE1 GLU A 166 CD CD A 402 1555 1555 2.32 LINK OE1 GLU A 177 CD CD A 403 1555 1555 2.44 LINK OE2 GLU A 177 CD CD A 404 1555 1555 2.45 LINK O ASN A 183 CD CD A 403 1555 1555 2.35 LINK OD2 ASP A 185 CD CD A 403 1555 1555 2.40 LINK OD1 ASP A 185 CD CD A 404 1555 1555 2.51 LINK O GLU A 187 CD CD A 404 1555 1555 2.38 LINK OE2 GLU A 190 CD CD A 403 1555 1555 2.34 LINK OE1 GLU A 190 CD CD A 404 1555 1555 2.54 LINK OE2 GLU A 190 CD CD A 404 1555 1555 2.51 LINK O TYR A 193 CA CA A 401 1555 1555 2.35 LINK O THR A 194 CA CA A 401 1555 1555 2.41 LINK OG1 THR A 194 CA CA A 401 1555 1555 2.40 LINK O ILE A 197 CA CA A 401 1555 1555 2.28 LINK OD1 ASP A 200 CA CA A 401 1555 1555 2.38 LINK CA CA A 401 O HOH A 630 1555 1555 2.39 LINK CA CA A 401 O HOH A 726 1555 1555 2.38 LINK CD CD A 402 O ALA B 30 1555 1555 2.43 LINK CD CD A 403 O HOH A 528 1555 1555 2.45 LINK CD CD A 403 O HOH A 533 1555 1555 2.42 LINK CD CD A 404 O HOH A 574 1555 1555 2.45 LINK CD CD A 405 O HOH A 538 1555 1555 2.39 LINK CD CD A 405 O HOH A 586 1555 1555 2.45 LINK CD CD A 405 O HOH A 779 1555 1555 2.36 CISPEP 1 LEU A 50 PRO A 51 0 3.46 SITE 1 AC1 6 TYR A 193 THR A 194 ILE A 197 ASP A 200 SITE 2 AC1 6 HOH A 630 HOH A 726 SITE 1 AC2 5 HIS A 142 GLU A 143 HIS A 146 GLU A 166 SITE 2 AC2 5 ALA B 30 SITE 1 AC3 6 GLU A 177 ASN A 183 ASP A 185 GLU A 190 SITE 2 AC3 6 HOH A 528 HOH A 533 SITE 1 AC4 6 ASP A 138 GLU A 177 ASP A 185 GLU A 187 SITE 2 AC4 6 GLU A 190 HOH A 574 SITE 1 AC5 6 ASP A 57 ASP A 59 GLN A 61 HOH A 538 SITE 2 AC5 6 HOH A 586 HOH A 779 SITE 1 AC6 3 HIS A 216 SER A 218 HOH A 874 CRYST1 93.488 93.488 129.558 90.00 90.00 120.00 P 61 2 2 12 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 0.010697 0.006176 0.000000 0.00000 SCALE2 0.000000 0.012351 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007719 0.00000