HEADER PROTEIN FIBRIL 07-JAN-11 3Q9J
TITLE AIIFL SEGMENT DERIVED FROM ALZHEIMER'S AMYLOID-BETA DISPLAYED ON 42-
TITLE 2 MEMBERED MACROCYCLE SCAFFOLD
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CYCLIC PSEUDO-PEPTIDE AIIFL(ORN)(HAO)YK(ORN);
COMPND 3 CHAIN: A, B, C, D, E, F, G, H;
COMPND 4 ENGINEERED: YES;
COMPND 5 MUTATION: YES;
COMPND 6 OTHER_DETAILS: AIIFL SEGMENT DERIVED FROM ALZHEIMER'S AMYLOID-BETA
COMPND 7 DISPLAYED ON 42-MEMBERED MACROCYCLE SCAFFOLD
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES
KEYWDS BETA SHEET TETRAMER, MACROCYCLIC PEPTIDE, BETA-SHEET MIMIC, AMYLOID-
KEYWDS 2 LIKE OLIGOMER, PROTEIN FIBRIL
EXPDTA X-RAY DIFFRACTION
AUTHOR C.LIU,M.R.SAWAYA,D.EISENBERG,J.S.NOWICK,P.CHENG,J.ZHENG
REVDAT 2 15-NOV-23 3Q9J 1 REMARK LINK ATOM
REVDAT 1 08-JUN-11 3Q9J 0
JRNL AUTH C.LIU,M.R.SAWAYA,P.N.CHENG,J.ZHENG,J.S.NOWICK,D.EISENBERG
JRNL TITL CHARACTERISTICS OF AMYLOID-RELATED OLIGOMERS REVEALED BY
JRNL TITL 2 CRYSTAL STRUCTURES OF MACROCYCLIC BETA-SHEET MIMICS.
JRNL REF J.AM.CHEM.SOC. V. 133 6736 2011
JRNL REFN ISSN 0002-7863
JRNL PMID 21473620
JRNL DOI 10.1021/JA200222N
REMARK 2
REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER-TNT
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SMART,VONRHEIN,WOMACK,
REMARK 3 : MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.18
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 3980
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.181
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : 0.223
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000
REMARK 3 FREE R VALUE TEST SET COUNT : 398
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 5
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.85
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1134
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.1980
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1021
REMARK 3 BIN R VALUE (WORKING SET) : 0.1889
REMARK 3 BIN FREE R VALUE : 0.2844
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.96
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 113
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 752
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 18
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 71.59
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 73.13
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -9.47620
REMARK 3 B22 (A**2) : -9.47620
REMARK 3 B33 (A**2) : 18.95230
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.437
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 871 ; 2.000 ; NULL
REMARK 3 BOND ANGLES : 1175 ; 2.000 ; NULL
REMARK 3 TORSION ANGLES : 190 ; 2.000 ; NULL
REMARK 3 TRIGONAL CARBON PLANES : 40 ; 2.000 ; NULL
REMARK 3 GENERAL PLANES : 200 ; 5.000 ; NULL
REMARK 3 ISOTROPIC THERMAL FACTORS : 623 ; 20.000 ; NULL
REMARK 3 BAD NON-BONDED CONTACTS : 1 ; 5.000 ; NULL
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 80 ; 5.000 ; NULL
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 947 ; 4.000 ; NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.12
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.15
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 20.73
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 8
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 3.4155 4.3118 15.1030
REMARK 3 T TENSOR
REMARK 3 T11: 0.1084 T22: -0.1724
REMARK 3 T33: -0.0506 T12: -0.3421
REMARK 3 T13: 0.1073 T23: -0.0309
REMARK 3 L TENSOR
REMARK 3 L11: 8.9649 L22: 4.5927
REMARK 3 L33: 1.6061 L12: 3.7864
REMARK 3 L13: 1.7221 L23: -2.9126
REMARK 3 S TENSOR
REMARK 3 S11: 0.3426 S12: -0.7893 S13: -0.1144
REMARK 3 S21: 0.4704 S22: 0.1666 S23: -0.0673
REMARK 3 S31: -0.4943 S32: 0.6822 S33: -0.5092
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { B|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 1.8700 5.1290 4.8661
REMARK 3 T TENSOR
REMARK 3 T11: 0.1890 T22: -0.1416
REMARK 3 T33: 0.0251 T12: -0.2146
REMARK 3 T13: 0.1123 T23: -0.0900
REMARK 3 L TENSOR
REMARK 3 L11: 2.3673 L22: 10.2100
REMARK 3 L33: 4.0423 L12: 4.8297
REMARK 3 L13: 3.9767 L23: -0.8727
REMARK 3 S TENSOR
REMARK 3 S11: 0.3149 S12: 0.4254 S13: -0.0762
REMARK 3 S21: -1.0768 S22: 0.4486 S23: 0.0940
REMARK 3 S31: -0.6458 S32: 0.0190 S33: -0.7635
REMARK 3
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: { C|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 12.3176 11.2509 10.7848
REMARK 3 T TENSOR
REMARK 3 T11: 0.1612 T22: -0.1201
REMARK 3 T33: 0.0930 T12: -0.3643
REMARK 3 T13: 0.1495 T23: -0.0545
REMARK 3 L TENSOR
REMARK 3 L11: -1.3337 L22: 1.6801
REMARK 3 L33: 1.0996 L12: 1.0170
REMARK 3 L13: -1.2402 L23: 2.8913
REMARK 3 S TENSOR
REMARK 3 S11: -0.4208 S12: 0.7050 S13: -0.8849
REMARK 3 S21: 0.3281 S22: 0.4713 S23: -0.3056
REMARK 3 S31: -0.5121 S32: 0.6570 S33: -0.0504
REMARK 3
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: { D|* }
REMARK 3 ORIGIN FOR THE GROUP (A): 3.5851 16.2562 9.1408
REMARK 3 T TENSOR
REMARK 3 T11: 0.1654 T22: -0.1068
REMARK 3 T33: 0.0569 T12: -0.3721
REMARK 3 T13: 0.0436 T23: -0.0973
REMARK 3 L TENSOR
REMARK 3 L11: 1.2240 L22: 7.4271
REMARK 3 L33: 0.0000 L12: -0.6395
REMARK 3 L13: -1.9452 L23: -2.6813
REMARK 3 S TENSOR
REMARK 3 S11: -0.3987 S12: 0.4165 S13: 0.0886
REMARK 3 S21: 0.3877 S22: 0.3449 S23: 0.6199
REMARK 3 S31: -0.5066 S32: 0.0625 S33: 0.0538
REMARK 3
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: { E|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -12.2325 -11.3152 10.8198
REMARK 3 T TENSOR
REMARK 3 T11: 0.0852 T22: -0.1019
REMARK 3 T33: 0.0553 T12: -0.4459
REMARK 3 T13: -0.1332 T23: 0.0698
REMARK 3 L TENSOR
REMARK 3 L11: 4.1205 L22: 6.6218
REMARK 3 L33: 0.0113 L12: -1.6028
REMARK 3 L13: 0.3283 L23: 4.7294
REMARK 3 S TENSOR
REMARK 3 S11: -0.1635 S12: 0.3146 S13: 0.8111
REMARK 3 S21: 0.4500 S22: 0.2257 S23: 0.4845
REMARK 3 S31: 0.5376 S32: -0.7096 S33: -0.0621
REMARK 3
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: { F|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -3.6263 -16.3093 9.0453
REMARK 3 T TENSOR
REMARK 3 T11: 0.1803 T22: -0.1247
REMARK 3 T33: 0.0459 T12: -0.3438
REMARK 3 T13: 0.0080 T23: 0.1353
REMARK 3 L TENSOR
REMARK 3 L11: 0.4595 L22: 11.3501
REMARK 3 L33: 0.1922 L12: 0.7052
REMARK 3 L13: 3.2573 L23: 1.7033
REMARK 3 S TENSOR
REMARK 3 S11: -0.5147 S12: 0.3408 S13: -0.1673
REMARK 3 S21: 0.4526 S22: 0.5270 S23: -0.6699
REMARK 3 S31: 0.7434 S32: 0.0979 S33: -0.0123
REMARK 3
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: { G|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -3.3033 -4.3045 15.0298
REMARK 3 T TENSOR
REMARK 3 T11: 0.1686 T22: -0.0798
REMARK 3 T33: -0.0104 T12: -0.3191
REMARK 3 T13: -0.1295 T23: 0.0746
REMARK 3 L TENSOR
REMARK 3 L11: 7.0062 L22: 6.7807
REMARK 3 L33: 6.9323 L12: 4.0025
REMARK 3 L13: 0.3736 L23: -0.2977
REMARK 3 S TENSOR
REMARK 3 S11: 0.3509 S12: -0.6264 S13: -0.0274
REMARK 3 S21: 0.4488 S22: 0.0090 S23: -0.2318
REMARK 3 S31: 0.7434 S32: -0.4911 S33: -0.3598
REMARK 3
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: { H|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -2.0254 -5.1108 4.8009
REMARK 3 T TENSOR
REMARK 3 T11: 0.2206 T22: -0.1381
REMARK 3 T33: -0.0224 T12: -0.2159
REMARK 3 T13: -0.1105 T23: 0.0612
REMARK 3 L TENSOR
REMARK 3 L11: 5.5760 L22: 12.3462
REMARK 3 L33: 3.7778 L12: 5.4878
REMARK 3 L13: 0.1004 L23: 0.0879
REMARK 3 S TENSOR
REMARK 3 S11: 0.1841 S12: 0.6923 S13: 0.0588
REMARK 3 S21: -0.9293 S22: 0.4325 S23: 0.2182
REMARK 3 S31: 0.5721 S32: -0.3330 S33: -0.6166
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3Q9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-11.
REMARK 100 THE DEPOSITION ID IS D_1000063364.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-APR-10
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 : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9197, 0.9129
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3979
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : 0.03900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.5700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.62
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.50900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SHELXE
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 58.76
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.98
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.00015 M ZINC ACETATE, 0.1M MES PH
REMARK 280 6.2, 12.5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE
REMARK 280 298K, PH 6.0
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31
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
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 21.02000
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 42.04000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 3040 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3390 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2940 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 3270 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -120.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H
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: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 HAO A 7 C - N - CA ANGL. DEV. = 19.4 DEGREES
REMARK 500 HAO A 7 CA - C - N ANGL. DEV. = 31.7 DEGREES
REMARK 500 HAO B 7 C - N - CA ANGL. DEV. = 19.1 DEGREES
REMARK 500 HAO B 7 CA - C - N ANGL. DEV. = 31.7 DEGREES
REMARK 500 HAO C 7 C - N - CA ANGL. DEV. = 18.2 DEGREES
REMARK 500 HAO C 7 CA - C - N ANGL. DEV. = 32.9 DEGREES
REMARK 500 HAO D 7 C - N - CA ANGL. DEV. = 19.7 DEGREES
REMARK 500 HAO D 7 CA - C - N ANGL. DEV. = 32.6 DEGREES
REMARK 500 HAO E 7 C - N - CA ANGL. DEV. = 18.9 DEGREES
REMARK 500 HAO E 7 CA - C - N ANGL. DEV. = 32.4 DEGREES
REMARK 500 HAO F 7 C - N - CA ANGL. DEV. = 19.6 DEGREES
REMARK 500 HAO F 7 CA - C - N ANGL. DEV. = 32.8 DEGREES
REMARK 500 HAO G 7 C - N - CA ANGL. DEV. = 17.6 DEGREES
REMARK 500 HAO G 7 CA - C - N ANGL. DEV. = 31.1 DEGREES
REMARK 500 HAO H 7 C - N - CA ANGL. DEV. = 19.0 DEGREES
REMARK 500 HAO H 7 CA - C - N ANGL. DEV. = 31.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 HAO B 7 -10.71
REMARK 500 HAO G 7 -10.32
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 ZN A 18 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN A 6 N
REMARK 620 2 ORN A 6 O 84.9
REMARK 620 3 ORN H 6 O 92.7 88.7
REMARK 620 4 ORN H 6 N 166.4 84.8 78.2
REMARK 620 5 HOH H 13 O 107.1 89.1 159.8 81.6
REMARK 620 6 HOH H 22 O 109.7 164.8 94.6 81.3 82.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 12 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN A 10 O
REMARK 620 2 ORN A 10 N 74.5
REMARK 620 3 ORN D 10 O 91.1 79.6
REMARK 620 4 ORN D 10 N 86.0 153.2 82.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 14 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN B 6 O
REMARK 620 2 ORN B 6 N 81.8
REMARK 620 3 HOH B 12 O 100.9 95.0
REMARK 620 4 ORN G 6 O 88.6 87.4 170.4
REMARK 620 5 ORN G 6 N 91.9 167.1 97.3 81.2
REMARK 620 6 HOH G 23 O 175.4 93.9 80.8 89.7 92.1
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN B 13 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN B 10 O
REMARK 620 2 ORN B 10 N 74.1
REMARK 620 3 ORN C 10 O 84.4 82.9
REMARK 620 4 ORN C 10 N 82.0 145.8 70.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN E 15 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN E 6 N
REMARK 620 2 ORN E 6 O 76.4
REMARK 620 N 1
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN E 19 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN E 10 O
REMARK 620 2 ORN E 10 N 79.4
REMARK 620 3 ORN H 10 O 85.8 84.8
REMARK 620 4 ORN H 10 N 75.8 147.4 72.7
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN F 16 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN F 6 N
REMARK 620 2 ORN F 6 O 77.8
REMARK 620 3 HOH F 14 O 99.3 79.0
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN F 17 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ORN F 10 O
REMARK 620 2 ORN F 10 N 73.9
REMARK 620 3 ORN G 10 O 85.6 80.5
REMARK 620 4 ORN G 10 N 83.3 147.4 74.8
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL E 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL D 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL C 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL F 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL G 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL H 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 11
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 12
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 13
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 14
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 15
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 16
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 17
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 18
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN E 19
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3Q9I RELATED DB: PDB
REMARK 900 A DIFFERENT SEGMENT OF AMYLOID BETA (LVFFA) DISPLAYED ON A SIMILAR
REMARK 900 MACROCYCLE FRAMEWORK
REMARK 900 RELATED ID: 3Q9H RELATED DB: PDB
REMARK 900 A DIFFERENT SEGMENT OF AMYLOID BETA (LVFFA) DISPLAYED ON A SIMILAR
REMARK 900 MACROCYCLE FRAMEWORK
REMARK 900 RELATED ID: 3Q9G RELATED DB: PDB
REMARK 900 A SEGMENT OF TAU (VQIVY) DISPLAYED ON A SIMILAR MACROCYCLE FRAMEWORK
DBREF 3Q9J A 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J B 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J C 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J D 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J E 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J F 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J G 1 10 PDB 3Q9J 3Q9J 1 10
DBREF 3Q9J H 1 10 PDB 3Q9J 3Q9J 1 10
SEQRES 1 A 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 B 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 C 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 D 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 E 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 F 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 G 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
SEQRES 1 H 10 ALA ILE ILE PHE LEU ORN HAO TYR LYS ORN
MODRES 3Q9J ORN A 6 ALA L-ORNITHINE
MODRES 3Q9J ORN A 10 ALA L-ORNITHINE
MODRES 3Q9J ORN B 6 ALA L-ORNITHINE
MODRES 3Q9J ORN B 10 ALA L-ORNITHINE
MODRES 3Q9J ORN C 6 ALA L-ORNITHINE
MODRES 3Q9J ORN C 10 ALA L-ORNITHINE
MODRES 3Q9J ORN D 6 ALA L-ORNITHINE
MODRES 3Q9J ORN D 10 ALA L-ORNITHINE
MODRES 3Q9J ORN E 6 ALA L-ORNITHINE
MODRES 3Q9J ORN E 10 ALA L-ORNITHINE
MODRES 3Q9J ORN F 6 ALA L-ORNITHINE
MODRES 3Q9J ORN F 10 ALA L-ORNITHINE
MODRES 3Q9J ORN G 6 ALA L-ORNITHINE
MODRES 3Q9J ORN G 10 ALA L-ORNITHINE
MODRES 3Q9J ORN H 6 ALA L-ORNITHINE
MODRES 3Q9J ORN H 10 ALA L-ORNITHINE
HET ORN A 6 8
HET HAO A 7 17
HET ORN A 10 8
HET ORN B 6 8
HET HAO B 7 17
HET ORN B 10 8
HET ORN C 6 8
HET HAO C 7 17
HET ORN C 10 8
HET ORN D 6 8
HET HAO D 7 17
HET ORN D 10 8
HET ORN E 6 8
HET HAO E 7 17
HET ORN E 10 8
HET ORN F 6 8
HET HAO F 7 17
HET ORN F 10 8
HET ORN G 6 8
HET HAO G 7 17
HET ORN G 10 8
HET ORN H 6 8
HET HAO H 7 17
HET ORN H 10 8
HET ZN A 12 1
HET ZN A 18 1
HET GOL B 11 6
HET ZN B 13 1
HET ZN B 14 1
HET CL C 11 1
HET CL D 11 1
HET CL E 11 1
HET ZN E 15 1
HET ZN E 19 1
HET CL F 11 1
HET ZN F 16 1
HET ZN F 17 1
HET GOL G 11 6
HET GOL H 11 6
HETNAM ORN L-ORNITHINE
HETNAM HAO {[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)
HETNAM 2 HAO ACETIC ACID
HETNAM ZN ZINC ION
HETNAM GOL GLYCEROL
HETNAM CL CHLORIDE ION
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 1 ORN 16(C5 H12 N2 O2)
FORMUL 1 HAO 8(C10 H11 N3 O5)
FORMUL 9 ZN 8(ZN 2+)
FORMUL 11 GOL 3(C3 H8 O3)
FORMUL 14 CL 4(CL 1-)
FORMUL 24 HOH *18(H2 O)
LINK N ALA A 1 C ORN A 10 1555 1555 1.24
LINK C LEU A 5 NE ORN A 6 1555 1555 1.29
LINK C ORN A 6 N HAO A 7 1555 1555 1.34
LINK C HAO A 7 N TYR A 8 1555 1555 1.35
LINK C LYS A 9 NE ORN A 10 1555 1555 1.40
LINK N ALA B 1 C ORN B 10 1555 1555 1.22
LINK C LEU B 5 NE ORN B 6 1555 1555 1.31
LINK C ORN B 6 N HAO B 7 1555 1555 1.32
LINK C HAO B 7 N TYR B 8 1555 1555 1.34
LINK C LYS B 9 NE ORN B 10 1555 1555 1.40
LINK N ALA C 1 C ORN C 10 1555 1555 1.25
LINK C LEU C 5 NE ORN C 6 1555 1555 1.33
LINK C ORN C 6 N HAO C 7 1555 1555 1.33
LINK C HAO C 7 N TYR C 8 1555 1555 1.35
LINK C LYS C 9 NE ORN C 10 1555 1555 1.41
LINK N ALA D 1 C ORN D 10 1555 1555 1.23
LINK C LEU D 5 NE ORN D 6 1555 1555 1.34
LINK C ORN D 6 N HAO D 7 1555 1555 1.31
LINK C HAO D 7 N TYR D 8 1555 1555 1.35
LINK C LYS D 9 NE ORN D 10 1555 1555 1.42
LINK N ALA E 1 C ORN E 10 1555 1555 1.24
LINK C LEU E 5 NE ORN E 6 1555 1555 1.35
LINK C ORN E 6 N HAO E 7 1555 1555 1.32
LINK C HAO E 7 N TYR E 8 1555 1555 1.35
LINK C LYS E 9 NE ORN E 10 1555 1555 1.41
LINK N ALA F 1 C ORN F 10 1555 1555 1.24
LINK C LEU F 5 NE ORN F 6 1555 1555 1.34
LINK C ORN F 6 N HAO F 7 1555 1555 1.31
LINK C HAO F 7 N TYR F 8 1555 1555 1.35
LINK C LYS F 9 NE ORN F 10 1555 1555 1.41
LINK N ALA G 1 C ORN G 10 1555 1555 1.23
LINK C LEU G 5 NE ORN G 6 1555 1555 1.30
LINK C ORN G 6 N HAO G 7 1555 1555 1.34
LINK C HAO G 7 N TYR G 8 1555 1555 1.32
LINK C LYS G 9 NE ORN G 10 1555 1555 1.40
LINK N ALA H 1 C ORN H 10 1555 1555 1.23
LINK C LEU H 5 NE ORN H 6 1555 1555 1.30
LINK C ORN H 6 N HAO H 7 1555 1555 1.34
LINK C HAO H 7 N TYR H 8 1555 1555 1.34
LINK C LYS H 9 NE ORN H 10 1555 1555 1.41
LINK N ORN A 6 ZN ZN A 18 1555 1555 1.99
LINK O ORN A 6 ZN ZN A 18 1555 1555 2.03
LINK O ORN A 10 ZN ZN A 12 1555 1555 1.94
LINK N ORN A 10 ZN ZN A 12 1555 1555 2.49
LINK ZN ZN A 12 O ORN D 10 1555 1555 1.89
LINK ZN ZN A 12 N ORN D 10 1555 1555 2.26
LINK ZN ZN A 18 O ORN H 6 1555 1555 1.98
LINK ZN ZN A 18 N ORN H 6 1555 1555 2.27
LINK ZN ZN A 18 O HOH H 13 1555 1555 2.61
LINK ZN ZN A 18 O HOH H 22 1555 1555 2.11
LINK O ORN B 6 ZN ZN B 14 1555 1555 1.98
LINK N ORN B 6 ZN ZN B 14 1555 1555 2.19
LINK O ORN B 10 ZN ZN B 13 1555 1555 2.03
LINK N ORN B 10 ZN ZN B 13 1555 1555 2.43
LINK O HOH B 12 ZN ZN B 14 1555 1555 2.55
LINK ZN ZN B 13 O ORN C 10 1555 1555 1.97
LINK ZN ZN B 13 N ORN C 10 1555 1555 2.65
LINK ZN ZN B 14 O ORN G 6 1555 1555 2.05
LINK ZN ZN B 14 N ORN G 6 1555 1555 2.15
LINK ZN ZN B 14 O HOH G 23 1555 1555 2.55
LINK N ORN E 6 ZN ZN E 15 1555 1555 2.19
LINK O ORN E 6 ZN ZN E 15 1555 1555 2.22
LINK O ORN E 10 ZN ZN E 19 1555 1555 1.97
LINK N ORN E 10 ZN ZN E 19 1555 1555 2.31
LINK ZN ZN E 19 O ORN H 10 1555 1555 1.99
LINK ZN ZN E 19 N ORN H 10 1555 1555 2.50
LINK N ORN F 6 ZN ZN F 16 1555 1555 2.11
LINK O ORN F 6 ZN ZN F 16 1555 1555 2.23
LINK O ORN F 10 ZN ZN F 17 1555 1555 1.98
LINK N ORN F 10 ZN ZN F 17 1555 1555 2.53
LINK O HOH F 14 ZN ZN F 16 1555 1555 1.91
LINK ZN ZN F 17 O ORN G 10 1555 1555 2.01
LINK ZN ZN F 17 N ORN G 10 1555 1555 2.42
SITE 1 AC1 1 LYS E 9
SITE 1 AC2 1 LYS D 9
SITE 1 AC3 1 LYS C 9
SITE 1 AC4 1 LYS F 9
SITE 1 AC5 5 HAO G 7 LYS G 9 HOH G 12 HOH G 13
SITE 2 AC5 5 HOH G 14
SITE 1 AC6 2 HAO B 7 TYR B 8
SITE 1 AC7 3 LYS B 9 LYS D 9 HOH G 15
SITE 1 AC8 2 ORN A 10 ORN D 10
SITE 1 AC9 2 ORN B 10 ORN C 10
SITE 1 BC1 4 ORN B 6 HOH B 12 ORN G 6 HOH G 23
SITE 1 BC2 2 ORN C 6 ORN E 6
SITE 1 BC3 3 ORN D 6 ORN F 6 HOH F 14
SITE 1 BC4 2 ORN F 10 ORN G 10
SITE 1 BC5 4 ORN A 6 ORN H 6 HOH H 13 HOH H 22
SITE 1 BC6 2 ORN E 10 ORN H 10
CRYST1 41.780 41.780 63.060 90.00 90.00 120.00 P 31 24
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 0.023935 0.013819 0.000000 0.00000
SCALE2 0.000000 0.027638 0.000000 0.00000
SCALE3 0.000000 0.000000 0.015858 0.00000