HEADER HYDROLASE 07-JAN-16 5FST
TITLE STRUCTURE OF LYSOZYME PREPARED BY THE 'SOAK-AND-FREEZE' METHOD UNDER
TITLE 2 100 BAR OF KRYPTON PRESSURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 19-147;
COMPND 5 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D IV;
COMPND 6 EC: 3.2.1.17
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS;
SOURCE 3 ORGANISM_COMMON: CHICKEN;
SOURCE 4 ORGANISM_TAXID: 9031
KEYWDS HYDROLASE, MURAMIDASE, LYSOZYME, KRYPTON, PRESSURE, FLASH FREEZING
EXPDTA X-RAY DIFFRACTION
AUTHOR B.LAFUMAT,C.MUELLER-DIECKMANN,N.COLLOC'H,T.PRANGE,A.ROYANT,P.VAN DER
AUTHOR 2 LINDEN,P.CARPENTIER
REVDAT 6 10-JAN-24 5FST 1 REMARK LINK
REVDAT 5 17-JUL-19 5FST 1 REMARK
REVDAT 4 21-FEB-18 5FST 1 AUTHOR JRNL
REVDAT 3 10-MAY-17 5FST 1 AUTHOR
REVDAT 2 16-NOV-16 5FST 1 TITLE
REVDAT 1 26-OCT-16 5FST 0
JRNL AUTH B.LAFUMAT,C.MUELLER-DIECKMANN,N.COLLOC'H,T.PRANGE,A.ROYANT,
JRNL AUTH 2 P.VAN DER LINDEN,P.CARPENTIER
JRNL TITL GAS-SENSITIVE BIOLOGICAL CRYSTALS PROCESSED IN PRESSURIZED
JRNL TITL 2 OXYGEN AND KRYPTON ATMOSPHERES: DECIPHERING GAS CHANNELS IN
JRNL TITL 3 PROTEINS USING A NOVEL `SOAK-AND-FREEZE' METHODOLOGY.
JRNL REF J.APPL.CRYSTALLOGR. V. 49 1478 2016
JRNL REFN ISSN 0021-8898
JRNL DOI 10.1107/S1600576716010992
REMARK 2
REMARK 2 RESOLUTION. 1.20 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0131
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.86
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 35416
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) : 0.110
REMARK 3 R VALUE (WORKING SET) : 0.109
REMARK 3 FREE R VALUE : 0.134
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 1798
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) : 1.20
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2548
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.11
REMARK 3 BIN R VALUE (WORKING SET) : 0.1240
REMARK 3 BIN FREE R VALUE SET COUNT : 134
REMARK 3 BIN FREE R VALUE : 0.1580
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 994
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 14
REMARK 3 SOLVENT ATOMS : 190
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.13
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): 0.031
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1130 ; 0.020 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 1050 ; 0.000 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1545 ; 2.042 ; 1.902
REMARK 3 BOND ANGLES OTHERS (DEGREES): 2392 ; 3.947 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 151 ; 6.328 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 58 ;35.121 ;22.586
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 188 ;11.628 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.583 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 158 ; 0.148 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1381 ; 0.013 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 312 ; 0.027 ; 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): 562 ; 1.521 ; 1.196
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 561 ; 1.523 ; 1.193
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 715 ; 1.919 ; 1.811
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 568 ; 3.086 ; 1.507
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): 2179 ;12.221 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 52 ;50.835 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2298 ;11.687 ; 5.000
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 : MASK
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: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS. HYDROGENS HAVE BEEN ADDED NOT REFINED
REMARK 4
REMARK 4 5FST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-JAN-16.
REMARK 100 THE DEPOSITION ID IS D_1290065964.
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 : 4.8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID29
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.864
REMARK 200 MONOCHROMATOR : SI111
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70048
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200
REMARK 200 RESOLUTION RANGE LOW (A) : 55.860
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.650
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 200 DATA REDUNDANCY : 13.80
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27
REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4
REMARK 200 DATA REDUNDANCY IN SHELL : 13.70
REMARK 200 R MERGE FOR SHELL (I) : 0.54000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.650
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 1LZ8
REMARK 200
REMARK 200 REMARK: ANOMALOUS DATA
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 41.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) NACL, 0.1M NA ACETATE PH 4.8
REMARK 280 25% (V/V) ETH-GLYCOL
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 18.52650
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.50050
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.50050
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.78975
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.50050
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.50050
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.26325
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.50050
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.50050
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.78975
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.50050
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.50050
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.26325
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 18.52650
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: 1740 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6630 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 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 KR KR A1132 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A2128 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 ARG A 61 NE CZ NH1 NH2
REMARK 470 LYS A 97 CD CE NZ
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 CL CL A 208 O HOH A 2123 0.13
REMARK 500 O HOH A 2035 O HOH A 2111 1.11
REMARK 500 HD22 ASN A 59 O HOH A 2114 1.25
REMARK 500 OD1 ASP A 18 O HOH A 2032 1.28
REMARK 500 O HOH A 2048 O HOH A 2053 1.28
REMARK 500 HG2 LYS A 97 O HOH A 2138 1.37
REMARK 500 HG2 LYS A 97 O HOH A 2137 1.41
REMARK 500 HB3 ASN A 44 O HOH A 2091 1.44
REMARK 500 O HOH A 2022 O HOH A 2071 1.50
REMARK 500 HH11 ARG A 45 OG1 THR A 51 1.52
REMARK 500 O HOH A 2068 O HOH A 2069 1.58
REMARK 500 O HOH A 2016 O HOH A 2188 1.62
REMARK 500 CG LYS A 97 O HOH A 2137 1.63
REMARK 500 O HOH A 2035 O HOH A 2169 1.64
REMARK 500 O HOH A 2111 O HOH A 2112 1.68
REMARK 500 O HOH A 2048 O HOH A 2049 1.72
REMARK 500 O HOH A 2137 O HOH A 2138 1.73
REMARK 500 O HOH A 2058 O HOH A 2144 1.73
REMARK 500 O HOH A 2014 O HOH A 2015 1.73
REMARK 500 O HOH A 2164 O HOH A 2165 1.77
REMARK 500 CD ARG A 61 O HOH A 2039 1.84
REMARK 500 CG LYS A 97 O HOH A 2138 1.92
REMARK 500 O HOH A 2075 O HOH A 2110 1.93
REMARK 500 ND2 ASN A 59 O HOH A 2114 1.95
REMARK 500 O HOH A 2021 O HOH A 2069 1.98
REMARK 500 O HOH A 2038 O HOH A 2039 1.99
REMARK 500 OD1 ASP A 48 O HOH A 2100 2.01
REMARK 500 O HOH A 2035 O HOH A 2112 2.04
REMARK 500 O HOH A 2038 O HOH A 2115 2.04
REMARK 500 O HOH A 2110 O HOH A 2111 2.06
REMARK 500 O HOH A 2161 O HOH A 2162 2.12
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 2026 O HOH A 2120 8554 0.73
REMARK 500 O THR A 43 HH21 ARG A 45 8554 1.21
REMARK 500 O HOH A 2082 O HOH A 2121 8554 1.28
REMARK 500 O THR A 43 HH22 ARG A 45 8554 1.47
REMARK 500 O THR A 43 NH2 ARG A 45 8554 1.52
REMARK 500 OD1 ASN A 44 HH22 ARG A 45 8554 1.60
REMARK 500 O HOH A 2078 O HOH A 2121 8554 1.64
REMARK 500 O HOH A 2046 O HOH A 2068 4555 1.64
REMARK 500 O HOH A 2046 O HOH A 2063 4555 2.09
REMARK 500 O HOH A 2011 O HOH A 2011 7554 2.17
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 ARG A 45 CG - CD - NE ANGL. DEV. = 19.9 DEGREES
REMARK 500 ILE A 55 CG1 - CB - CG2 ANGL. DEV. = -13.8 DEGREES
REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 615
REMARK 615 ZERO OCCUPANCY ATOM
REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 615 M RES C SSEQI
REMARK 615 CL A 208
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 209 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 SER A 60 O
REMARK 620 2 CYS A 64 O 90.6
REMARK 620 3 SER A 72 OG 88.6 169.7
REMARK 620 4 ARG A 73 O 92.4 90.3 100.0
REMARK 620 5 HOH A2117 O 100.5 88.9 81.1 167.1
REMARK 620 6 HOH A2118 O 172.6 96.7 84.0 89.0 78.3
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 201
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 203
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 204
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL 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 NA A 209
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KR A 1130
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KR A 1131
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KR A 1132
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KR A 1133
REMARK 800
REMARK 800 SITE_IDENTIFIER: BC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KR A 1134
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5FSJ RELATED DB: PDB
REMARK 900 THERMOLYSIN SOAK-AND-FREEZE UNDER 45BAR DIOXYGEN
REMARK 900 RELATED ID: 5FSP RELATED DB: PDB
REMARK 900 THERMOLYSIN SOAK-AND-FREEZE UNDER 100BAR KRYPTON
REMARK 900 RELATED ID: 5FSS RELATED DB: PDB
REMARK 900 THERMOLYSIN SOAK-AND-FREEZE UNDER 40BAR OF KRYPTON
DBREF 5FST A 1 129 UNP P00698 LYSC_CHICK 19 147
SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
HET CL A 201 1
HET CL A 202 1
HET CL A 203 1
HET CL A 204 1
HET CL A 205 1
HET CL A 206 1
HET CL A 207 1
HET CL A 208 1
HET NA A 209 1
HET KR A1130 1
HET KR A1131 1
HET KR A1132 1
HET KR A1133 1
HET KR A1134 1
HETNAM CL CHLORIDE ION
HETNAM NA SODIUM ION
HETNAM KR KRYPTON
FORMUL 2 CL 8(CL 1-)
FORMUL 10 NA NA 1+
FORMUL 11 KR 5(KR)
FORMUL 16 HOH *190(H2 O)
HELIX 1 1 GLY A 4 HIS A 15 1 12
HELIX 2 2 SER A 24 ASN A 37 1 14
HELIX 3 3 CYS A 80 SER A 85 5 6
HELIX 4 4 ILE A 88 SER A 100 1 13
HELIX 5 5 ASN A 103 ALA A 107 5 5
HELIX 6 6 TRP A 108 CYS A 115 1 8
HELIX 7 7 ASP A 119 ARG A 125 5 7
SHEET 1 AA 3 THR A 43 ARG A 45 0
SHEET 2 AA 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44
SHEET 3 AA 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53
SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.05
SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.07
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.07
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.04
LINK O SER A 60 NA NA A 209 1555 1555 2.32
LINK O CYS A 64 NA NA A 209 1555 1555 2.42
LINK OG SER A 72 NA NA A 209 1555 1555 2.49
LINK O ARG A 73 NA NA A 209 1555 1555 2.42
LINK NA NA A 209 O HOH A2117 1555 1555 2.46
LINK NA NA A 209 O HOH A2118 1555 1555 2.44
SITE 1 AC1 2 TYR A 23 ASN A 113
SITE 1 AC2 4 SER A 24 GLY A 26 GLN A 121 HOH A2047
SITE 1 AC3 4 GLY A 67 ARG A 68 THR A 69 SER A 72
SITE 1 AC4 3 ILE A 88 HOH A2009 HOH A2025
SITE 1 AC5 2 LYS A 33 PHE A 38
SITE 1 AC6 2 ASN A 65 PRO A 79
SITE 1 AC7 2 ARG A 73 ASN A 74
SITE 1 AC8 6 SER A 60 CYS A 64 SER A 72 ARG A 73
SITE 2 AC8 6 HOH A2117 HOH A2118
SITE 1 AC9 2 ARG A 14 HIS A 15
SITE 1 BC1 2 ILE A 55 VAL A 92
SITE 1 BC2 2 THR A 43 HOH A2096
SITE 1 BC3 4 GLN A 41 TYR A 53 SER A 81 LEU A 84
SITE 1 BC4 2 ARG A 14 ARG A 128
CRYST1 79.001 79.001 37.053 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 0.026988 0.00000
(ATOM LINES ARE NOT SHOWN.)
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