PDB Short entry for 2YMK HEADER ANTIBIOTIC 09-OCT-12 2YMK TITLE CRYSTAL STRUCTURE OF THE HEXAMERIC ANTI-MICROBIAL PEPTIDE TITLE 2 CHANNEL DERMCIDIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DCD-1; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: PEPTIDE, RESIDUES 63-110; COMPND 5 SYNONYM: DERMCIDIN, PREPROTEOLYSIN, SURVIVAL-PROMOTING PEPTIDE; COMPND 6 EC: 3.4.-.-; COMPND 7 OTHER_DETAILS: PEPTIDE OF 48 RESIDUES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS ANTIBIOTIC, ANTI-MICROBIAL PEPTIDE CHANNEL, MEMBRANE SPANNING KEYWDS 2 PEPTIDE, HUMAN EPIDERMAL SURFACE EXPDTA X-RAY DIFFRACTION AUTHOR K.ZETH REVDAT 4 25-DEC-13 2YMK 1 COMPND JRNL REVDAT 3 03-APR-13 2YMK 1 JRNL REVDAT 2 06-MAR-13 2YMK 1 JRNL REMARK REVDAT 1 17-OCT-12 2YMK 0 JRNL AUTH C.SONG,C.WEICHBRODT,E.S.SALNIKOV,M.DYNOWSKI,B.O.FORSBERG, JRNL AUTH 2 B.BECHINGER,C.STEINEM,B.L.DE GROOT,U.ZACHARIAE,K.ZETH JRNL TITL CRYSTAL STRUCTURE AND FUNCTIONAL MECHANISM OF A HUMAN JRNL TITL 2 ANTIMICROBIAL MEMBRANE CHANNEL. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 4586 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 23426625 JRNL DOI 10.1073/PNAS.1214739110 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.82 REMARK 3 NUMBER OF REFLECTIONS : 5189 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) : 0.20838 REMARK 3 R VALUE (WORKING SET) : 0.20466 REMARK 3 FREE R VALUE : 0.27384 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.6 REMARK 3 FREE R VALUE TEST SET COUNT : 252 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.493 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.558 REMARK 3 REFLECTION IN BIN (WORKING SET) : 349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.234 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.267 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 980 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.651 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -50.26 REMARK 3 B22 (A**2) : 21.97 REMARK 3 B33 (A**2) : 28.29 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 42.34 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.245 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.582 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 980 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1307 ; 2.333 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 137 ; 7.754 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;29.181 ;29.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 194 ;24.401 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 160 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 674 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 673 ; 0.867 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1046 ; 1.613 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 307 ; 2.083 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 261 ; 3.784 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 2 A 48 4 REMARK 3 1 B 2 B 48 4 REMARK 3 1 C 2 C 48 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 318 ; 0.38 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 318 ; 0.45 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 C (A): 318 ; 0.48 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 318 ; 0.83 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 318 ; 0.88 ; 2.00 REMARK 3 MEDIUM THERMAL 1 C (A**2): 318 ; 0.67 ; 2.00 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 3 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.328 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -0.500H+0.500K+L, 0.500H-0.500K+L, 0.500H+0.50 REMARK 3 TWIN FRACTION : 0.268 REMARK 3 TWIN DOMAIN : 3 REMARK 3 TWIN OPERATOR : -0.500H-0.500K+L, -0.500H-0.500K-L, 0.500H-0.50 REMARK 3 TWIN FRACTION : 0.403 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 48 REMARK 3 ORIGIN FOR THE GROUP (A): -11.0071 32.4357 9.3482 REMARK 3 T TENSOR REMARK 3 T11: 0.2763 T22: 0.1843 REMARK 3 T33: 0.1683 T12: 0.0302 REMARK 3 T13: -0.0804 T23: 0.0159 REMARK 3 L TENSOR REMARK 3 L11: 23.3757 L22: 0.8216 REMARK 3 L33: 3.2015 L12: 0.9891 REMARK 3 L13: -7.6477 L23: -0.1003 REMARK 3 S TENSOR REMARK 3 S11: 0.6065 S12: -0.2339 S13: -0.7673 REMARK 3 S21: 0.1665 S22: -0.4438 S23: -0.0748 REMARK 3 S31: -0.2649 S32: 0.1321 S33: -0.1627 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 48 REMARK 3 ORIGIN FOR THE GROUP (A): -4.7870 22.6749 22.5494 REMARK 3 T TENSOR REMARK 3 T11: 0.2874 T22: 0.1588 REMARK 3 T33: 0.2289 T12: -0.0054 REMARK 3 T13: -0.0719 T23: -0.0419 REMARK 3 L TENSOR REMARK 3 L11: 20.5597 L22: 0.7938 REMARK 3 L33: 5.6204 L12: 0.3320 REMARK 3 L13: -10.1188 L23: 0.0376 REMARK 3 S TENSOR REMARK 3 S11: 1.1283 S12: -0.3778 S13: 0.3963 REMARK 3 S21: 0.0200 S22: -0.5777 S23: -0.0676 REMARK 3 S31: -0.9228 S32: 0.2419 S33: -0.5505 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 3 C 48 REMARK 3 ORIGIN FOR THE GROUP (A): -4.5679 40.2994 23.8052 REMARK 3 T TENSOR REMARK 3 T11: 0.2658 T22: 0.2085 REMARK 3 T33: 0.1110 T12: -0.0073 REMARK 3 T13: -0.1018 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 21.1139 L22: 1.4125 REMARK 3 L33: 3.1177 L12: -2.1127 REMARK 3 L13: -7.4740 L23: 0.7043 REMARK 3 S TENSOR REMARK 3 S11: 0.5495 S12: 0.7708 S13: 0.0594 REMARK 3 S21: -0.1240 S22: -0.2946 S23: -0.0900 REMARK 3 S31: -0.3434 S32: -0.2392 S33: -0.2549 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 2YMK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-OCT-12. REMARK 100 THE PDBE ID CODE IS EBI-54418. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL (PILATUS 6M) REMARK 200 DETECTOR MANUFACTURER : DECTRIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5189 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.50 REMARK 200 RESOLUTION RANGE LOW (A) : 33.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.2 REMARK 200 R MERGE (I) : 0.02 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.1 REMARK 200 R MERGE FOR SHELL (I) : 0.51 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.95 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP, DM, BUCCANEER REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M ZN(AC)2, 0.1 M REMARK 280 NA-CACODYLATE, 18% PEG8000 AT PH 6.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.17700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.36200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.17700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.36200 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -423.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 BIOMT1 2 -1.000000 0.000000 0.000000 -21.28921 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.48128 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 1 REMARK 465 SER A 2 REMARK 465 SER B 1 REMARK 465 SER C 1 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 LEU C 21 CG CD1 CD2 REMARK 470 LYS C 41 CG CD CE NZ 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 VAL C 37 CB - CA - C ANGL. DEV. = -11.6 DEGREES 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 VAL A 32 -81.08 -48.92 REMARK 500 LEU A 44 2.26 -62.14 REMARK 500 SER A 46 9.71 -67.16 REMARK 500 ALA B 25 -56.61 -28.44 REMARK 500 VAL B 26 -71.67 -62.17 REMARK 500 GLU B 27 -48.38 -26.52 REMARK 500 VAL B 37 -73.47 -46.10 REMARK 500 LEU C 44 24.81 -72.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU B 30 23.3 L L OUTSIDE RANGE 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 A1049 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 42 OD2 REMARK 620 2 HIS A 38 NE2 108.2 REMARK 620 3 GLU B 5 OE2 119.5 110.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1050 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A2003 O REMARK 620 2 ASP A 28 OD2 123.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1049 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 9 OD2 REMARK 620 2 ASP B 42 OD2 83.1 REMARK 620 3 HIS B 38 NE2 100.6 127.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1050 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 28 OD2 REMARK 620 2 HOH B2002 O 136.1 REMARK 620 3 HOH B2009 O 88.4 116.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1049 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 5 OE1 REMARK 620 2 HIS C 38 NE2 120.2 REMARK 620 3 ASP C 42 OD1 90.9 111.6 REMARK 620 4 ASP C 9 OD2 104.3 92.3 140.3 REMARK 620 5 ASP C 42 OD2 113.5 125.0 55.2 85.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1050 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 28 OD2 REMARK 620 2 HOH C2005 O 102.9 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 ZN A1049 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1049 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1049 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1050 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1050 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1050 DBREF 2YMK A 1 48 UNP P81605 DCD_HUMAN 63 110 DBREF 2YMK B 1 48 UNP P81605 DCD_HUMAN 63 110 DBREF 2YMK C 1 48 UNP P81605 DCD_HUMAN 63 110 SEQRES 1 A 48 SER SER LEU LEU GLU LYS GLY LEU ASP GLY ALA LYS LYS SEQRES 2 A 48 ALA VAL GLY GLY LEU GLY LYS LEU GLY LYS ASP ALA VAL SEQRES 3 A 48 GLU ASP LEU GLU SER VAL GLY LYS GLY ALA VAL HIS ASP SEQRES 4 A 48 VAL LYS ASP VAL LEU ASP SER VAL LEU SEQRES 1 B 48 SER SER LEU LEU GLU LYS GLY LEU ASP GLY ALA LYS LYS SEQRES 2 B 48 ALA VAL GLY GLY LEU GLY LYS LEU GLY LYS ASP ALA VAL SEQRES 3 B 48 GLU ASP LEU GLU SER VAL GLY LYS GLY ALA VAL HIS ASP SEQRES 4 B 48 VAL LYS ASP VAL LEU ASP SER VAL LEU SEQRES 1 C 48 SER SER LEU LEU GLU LYS GLY LEU ASP GLY ALA LYS LYS SEQRES 2 C 48 ALA VAL GLY GLY LEU GLY LYS LEU GLY LYS ASP ALA VAL SEQRES 3 C 48 GLU ASP LEU GLU SER VAL GLY LYS GLY ALA VAL HIS ASP SEQRES 4 C 48 VAL LYS ASP VAL LEU ASP SER VAL LEU HET ZN A1049 1 HET ZN B1049 1 HET ZN C1049 1 HET ZN A1050 1 HET ZN B1050 1 HET ZN C1050 1 HETNAM ZN ZINC ION FORMUL 4 ZN 6(ZN 2+) FORMUL 5 HOH *24(H2 O) HELIX 1 1 LEU A 4 SER A 46 1 43 HELIX 2 2 SER B 2 SER B 46 1 45 HELIX 3 3 SER C 2 VAL C 47 1 46 LINK ZN ZN A1049 OD2 ASP A 42 1555 1555 1.87 LINK ZN ZN A1049 NE2 HIS A 38 1555 1555 2.38 LINK ZN ZN A1049 OE2 GLU B 5 1555 2556 2.42 LINK ZN ZN A1050 O HOH A2003 1555 1555 2.26 LINK ZN ZN A1050 OD2 ASP A 28 1555 1555 2.26 LINK OD2 ASP B 9 ZN ZN A1049 1555 2556 1.67 LINK OD2 ASP B 9 ZN ZN A1049 2556 1555 1.67 LINK ZN ZN B1049 NE2 HIS B 38 1555 1555 2.37 LINK ZN ZN B1049 OD2 ASP B 42 1555 1555 2.32 LINK ZN ZN B1049 OD2 ASP A 9 1555 2556 1.94 LINK ZN ZN B1050 O HOH B2009 1555 1555 2.66 LINK ZN ZN B1050 O HOH B2002 1555 1555 2.55 LINK ZN ZN B1050 OD2 ASP B 28 1555 1555 2.62 LINK ZN ZN C1049 OD2 ASP C 9 1555 2556 2.19 LINK ZN ZN C1049 OD2 ASP C 42 1555 1555 2.02 LINK ZN ZN C1049 OD1 ASP C 42 1555 1555 2.55 LINK ZN ZN C1049 NE2 HIS C 38 1555 1555 2.25 LINK ZN ZN C1049 OE1 GLU C 5 1555 2556 2.47 LINK ZN ZN C1050 O HOH C2005 1555 1555 2.43 LINK ZN ZN C1050 OD2 ASP C 28 1555 1555 2.59 SITE 1 AC1 4 HIS A 38 ASP A 42 GLU B 5 ASP B 9 SITE 1 AC2 4 GLU A 5 ASP A 9 HIS B 38 ASP B 42 SITE 1 AC3 4 GLU C 5 ASP C 9 HIS C 38 ASP C 42 SITE 1 AC4 5 ASP A 24 ASP A 28 HOH A2003 LYS B 6 SITE 2 AC4 5 LYS B 20 SITE 1 AC5 4 ASP B 24 ASP B 28 HOH B2002 HOH B2009 SITE 1 AC6 3 ASP C 24 ASP C 28 HOH C2005 CRYST1 76.354 50.724 45.738 90.00 117.74 90.00 C 1 2 1 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 0.013097 0.000000 0.006888 0.00000 SCALE2 0.000000 0.019715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024703 0.00000