HEADER HYDROLASE 04-SEP-19 6SR4 TITLE X-RAY PUMP X-RAY PROBE ON LYSOZYME.GD NANOCRYSTALS: 112 FS TIME DELAY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV; COMPND 5 EC: 3.2.1.17; COMPND 6 OTHER_DETAILS: CYSTEINE RESIDUES WERE MODELED AS ALANINES AND NON- COMPND 7 COVALENT SULFUR ATOM. THE PROTEIN CONTAINS A GD COMPOUND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS RADIATION DAMAGE, SERIAL FEMTOSECOND CRYSTALLOGRAPHY, X-RAY FREE- KEYWDS 2 ELECTRON LASER, TIME-RESOLVED CRYSTALLOGRAPHY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KLOOS,A.GOREL,K.NASS REVDAT 2 24-JAN-24 6SR4 1 LINK REVDAT 1 22-APR-20 6SR4 0 JRNL AUTH K.NASS,A.GOREL,M.M.ABDULLAH,A.V MARTIN,M.KLOOS,A.MARINELLI, JRNL AUTH 2 A.AQUILA,T.R.M.BARENDS,F.J.DECKER,R.BRUCE DOAK,L.FOUCAR, JRNL AUTH 3 E.HARTMANN,M.HILPERT,M.S.HUNTER,Z.JUREK,J.E.KOGLIN,A.KOZLOV, JRNL AUTH 4 A.A.LUTMAN,G.N.KOVACS,C.M.ROOME,R.L.SHOEMAN,R.SANTRA, JRNL AUTH 5 H.M.QUINEY,B.ZIAJA,S.BOUTET,I.SCHLICHTING JRNL TITL STRUCTURAL DYNAMICS IN PROTEINS INDUCED BY AND PROBED WITH JRNL TITL 2 X-RAY FREE-ELECTRON LASER PULSES. JRNL REF NAT COMMUN V. 11 1814 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32286284 JRNL DOI 10.1038/S41467-020-15610-4 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5315 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 591 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 392 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2020 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.518 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.299 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.880 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.876 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1060 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 961 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1432 ; 1.680 ; 1.669 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2210 ; 1.170 ; 1.678 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 127 ; 7.365 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 61 ;31.904 ;20.656 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 156 ;13.704 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;20.207 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 131 ; 0.063 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1208 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 249 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REMARK 3 REFINED INDIVIDUALLY REMARK 3 THE SUBMITTED COORDINATES REPRESENT THE MEAN OF 100 COORDINATE REMARK 3 SETS OBTAINED BY REFINING AGAINST 100 DIFFERENT INTEGRATED REMARK 3 DIFFRACTION INTENSITY DATASETS OBTAINED BY JACKKNIFE RESAMPLING OF REMARK 3 THE DIFFRACTION SNAPSHOTS. THE COORDINATE HEADER ORIGINATES FROM REMARK 3 ONE OF THE INDIVIDUAL REFINEMENTS. REMARK 3 CYSTEINE RESIDUES WERE MODELED AS ALANINES AND NON-COVALENTLY REMARK 3 ATTACHED SULPHUR ATOMS. REMARK 4 REMARK 4 6SR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 3.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.75 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5315 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.320 REMARK 200 RESOLUTION RANGE LOW (A) : 22.810 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 FOR SHELL : 7.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4N5R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % NACL, 6 % PEG 6000, 0.1 M SODIUM REMARK 280 ACETATE PH 3.0, BATCH MODE, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 19.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.62500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.87500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.62500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.87500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 19.75000 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 TOTAL BURIED SURFACE AREA: 1560 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL 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 MET A -17 REMARK 465 ARG A -16 REMARK 465 SER A -15 REMARK 465 LEU A -14 REMARK 465 LEU A -13 REMARK 465 ILE A -12 REMARK 465 LEU A -11 REMARK 465 VAL A -10 REMARK 465 LEU A -9 REMARK 465 CYS A -8 REMARK 465 PHE A -7 REMARK 465 LEU A -6 REMARK 465 PRO A -5 REMARK 465 LEU A -4 REMARK 465 ALA A -3 REMARK 465 ALA A -2 REMARK 465 LEU A -1 REMARK 465 GLY A 0 REMARK 465 LEU A 129 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 GD GD A 202 O7 DO3 A 203 1.83 REMARK 500 GD GD A 201 O3 DO3 A 204 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 6 CB CYS A 6 SG 0.938 REMARK 500 CYS A 30 CB CYS A 30 SG 0.722 REMARK 500 TRP A 63 CE3 TRP A 63 CZ3 -0.203 REMARK 500 TRP A 63 CZ3 TRP A 63 CH2 0.130 REMARK 500 CYS A 64 CB CYS A 64 SG 0.956 REMARK 500 CYS A 76 CB CYS A 76 SG 0.919 REMARK 500 CYS A 80 CB CYS A 80 SG 0.507 REMARK 500 CYS A 94 CB CYS A 94 SG 0.817 REMARK 500 CYS A 115 CB CYS A 115 SG 0.729 REMARK 500 CYS A 127 CB CYS A 127 SG 0.592 REMARK 500 REMARK 500 REMARK: NULL 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 CYS A 30 CA - CB - SG ANGL. DEV. = -16.6 DEGREES REMARK 500 TRP A 63 CD2 - CE3 - CZ3 ANGL. DEV. = -34.2 DEGREES REMARK 500 TRP A 63 CZ3 - CH2 - CZ2 ANGL. DEV. = -33.4 DEGREES REMARK 500 CYS A 76 CA - CB - SG ANGL. DEV. = -21.2 DEGREES REMARK 500 CYS A 115 CA - CB - SG ANGL. DEV. = 15.8 DEGREES REMARK 500 CYS A 127 CA - CB - SG ANGL. DEV. = 23.8 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 ASN A 37 33.64 71.54 REMARK 500 ARG A 68 16.77 -145.52 REMARK 500 CYS A 115 -40.45 -133.44 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 NA A 205 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 60 O REMARK 620 2 CYS A 64 O 79.8 REMARK 620 3 SER A 72 OG 89.3 155.9 REMARK 620 4 ARG A 73 O 96.2 99.7 102.8 REMARK 620 5 HOH A 312 O 169.0 108.9 80.1 89.1 REMARK 620 6 HOH A 323 O 97.7 89.3 70.9 164.6 76.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 GD A 201 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DO3 A 204 N2 REMARK 620 2 DO3 A 204 N3 67.6 REMARK 620 3 DO3 A 204 O5 117.1 58.7 REMARK 620 4 DO3 A 204 O1 95.7 163.3 135.2 REMARK 620 5 DO3 A 204 N1 74.5 101.4 143.2 71.8 REMARK 620 6 DO3 A 204 N4 107.2 65.1 78.3 122.1 64.9 REMARK 620 7 DO3 A 204 O7 150.9 114.7 84.2 79.2 76.6 55.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 GD A 202 GD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DO3 A 203 N2 REMARK 620 2 DO3 A 203 N3 65.1 REMARK 620 3 DO3 A 203 O3 66.1 95.8 REMARK 620 4 DO3 A 203 O5 114.4 63.1 82.0 REMARK 620 5 DO3 A 203 N1 63.1 99.4 113.1 158.8 REMARK 620 6 DO3 A 203 N4 100.1 67.4 162.2 94.7 66.3 REMARK 620 7 DO3 A 203 O1 92.8 155.6 83.5 140.2 59.3 109.2 REMARK 620 8 HOH A 303 O 128.1 136.3 65.2 75.1 124.0 131.0 65.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GD A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GD A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DO3 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DO3 A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 208 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RS0 RELATED DB: PDB REMARK 900 SINGLE PULSE REFERENCE DATA SET REMARK 900 RELATED ID: 6SR1 RELATED DB: PDB REMARK 900 35 FS TIME DELAY REMARK 900 RELATED ID: 6SR2 RELATED DB: PDB REMARK 900 37 FS TIME DELAY REMARK 900 RELATED ID: 6SR3 RELATED DB: PDB REMARK 900 62 FS TIME DELAY REMARK 900 RELATED ID: 6SR5 RELATED DB: PDB REMARK 900 102 FS TIME DELAY DBREF 6SR4 A -17 129 UNP P00698 LYSC_CHICK 1 147 SEQRES 1 A 147 MET ARG SER LEU LEU ILE LEU VAL LEU CYS PHE LEU PRO SEQRES 2 A 147 LEU ALA ALA LEU GLY LYS VAL PHE GLY ARG CYS GLU LEU SEQRES 3 A 147 ALA ALA ALA MET LYS ARG HIS GLY LEU ASP ASN TYR ARG SEQRES 4 A 147 GLY TYR SER LEU GLY ASN TRP VAL CYS ALA ALA LYS PHE SEQRES 5 A 147 GLU SER ASN PHE ASN THR GLN ALA THR ASN ARG ASN THR SEQRES 6 A 147 ASP GLY SER THR ASP TYR GLY ILE LEU GLN ILE ASN SER SEQRES 7 A 147 ARG TRP TRP CYS ASN ASP GLY ARG THR PRO GLY SER ARG SEQRES 8 A 147 ASN LEU CYS ASN ILE PRO CYS SER ALA LEU LEU SER SER SEQRES 9 A 147 ASP ILE THR ALA SER VAL ASN CYS ALA LYS LYS ILE VAL SEQRES 10 A 147 SER ASP GLY ASN GLY MET ASN ALA TRP VAL ALA TRP ARG SEQRES 11 A 147 ASN ARG CYS LYS GLY THR ASP VAL GLN ALA TRP ILE ARG SEQRES 12 A 147 GLY CYS ARG LEU HET GD A 201 1 HET GD A 202 1 HET DO3 A 203 28 HET DO3 A 204 28 HET NA A 205 1 HET CL A 206 1 HET CL A 207 1 HET CL A 208 1 HETNAM GD GADOLINIUM ATOM HETNAM DO3 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10- HETNAM 2 DO3 TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 GD 2(GD) FORMUL 4 DO3 2(C17 H32 N4 O7) FORMUL 6 NA NA 1+ FORMUL 7 CL 3(CL 1-) FORMUL 10 HOH *26(H2 O) HELIX 1 AA1 GLY A 4 HIS A 15 1 12 HELIX 2 AA2 ASN A 19 TYR A 23 5 5 HELIX 3 AA3 SER A 24 ASN A 37 1 14 HELIX 4 AA4 PRO A 79 SER A 85 5 7 HELIX 5 AA5 ILE A 88 SER A 100 1 13 HELIX 6 AA6 ASN A 103 ALA A 107 5 5 HELIX 7 AA7 TRP A 108 CYS A 115 1 8 HELIX 8 AA8 ASP A 119 ARG A 125 5 7 SHEET 1 AA1 3 THR A 43 ARG A 45 0 SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44 SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53 LINK O SER A 60 NA NA A 205 1555 1555 2.53 LINK O CYS A 64 NA NA A 205 1555 1555 2.48 LINK OG SER A 72 NA NA A 205 1555 1555 2.69 LINK O ARG A 73 NA NA A 205 1555 1555 2.71 LINK GD GD A 201 N2 DO3 A 204 1555 1555 2.69 LINK GD GD A 201 N3 DO3 A 204 1555 1555 2.86 LINK GD GD A 201 O5 DO3 A 204 1555 1555 3.03 LINK GD GD A 201 O1 DO3 A 204 1555 1555 2.89 LINK GD GD A 201 N1 DO3 A 204 1555 1555 2.32 LINK GD GD A 201 N4 DO3 A 204 1555 1555 2.99 LINK GD GD A 201 O7 DO3 A 204 1555 1555 3.14 LINK GD GD A 202 N2 DO3 A 203 1555 1555 2.79 LINK GD GD A 202 N3 DO3 A 203 1555 1555 2.82 LINK GD GD A 202 O3 DO3 A 203 1555 1555 2.35 LINK GD GD A 202 O5 DO3 A 203 1555 1555 2.30 LINK GD GD A 202 N1 DO3 A 203 1555 1555 2.91 LINK GD GD A 202 N4 DO3 A 203 1555 1555 2.80 LINK GD GD A 202 O1 DO3 A 203 1555 1555 2.34 LINK GD GD A 202 O HOH A 303 1555 1555 2.93 LINK NA NA A 205 O HOH A 312 1555 1555 2.59 LINK NA NA A 205 O HOH A 323 1555 1555 2.71 SITE 1 AC1 1 DO3 A 204 SITE 1 AC2 2 DO3 A 203 HOH A 303 SITE 1 AC3 8 TRP A 62 ASN A 103 ASP A 119 GLN A 121 SITE 2 AC3 8 ARG A 125 GD A 202 DO3 A 204 HOH A 303 SITE 1 AC4 8 ARG A 5 GLY A 117 THR A 118 ASP A 119 SITE 2 AC4 8 TRP A 123 GD A 201 DO3 A 203 HOH A 303 SITE 1 AC5 6 SER A 60 CYS A 64 SER A 72 ARG A 73 SITE 2 AC5 6 HOH A 312 HOH A 323 SITE 1 AC6 2 TYR A 23 ASN A 113 SITE 1 AC7 3 SER A 24 GLY A 26 GLN A 121 SITE 1 AC8 4 GLY A 67 ARG A 68 THR A 69 HOH A 323 CRYST1 79.000 79.000 39.500 90.00 90.00 90.00 P 43 21 2 8 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 0.012658 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012658 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025316 0.00000