HEADER TRANSPORT PROTEIN 01-JUL-22 8AAQ TITLE CRYSTAL STRUCTURE OF THE CAROTENOID-BINDING PROTEIN DOMAIN FROM TITLE 2 SILKWORM BOMBYX MORI (BMCBP), CRT-416 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAROTENOID-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOMBYX MORI; SOURCE 3 ORGANISM_COMMON: DOMESTIC SILKWORM; SOURCE 4 ORGANISM_TAXID: 7091; SOURCE 5 GENE: BMCBP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CAROTENOID-BINDING PROTEIN, CAROTENOID TRANSPORT, CBP, STARD, START KEYWDS 2 DOMAIN, BOMBYX MORI, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.A.VARFOLOMEEVA,Y.B.SLONIMSKIY,N.A.EGORKIN,M.E.MINYAEV,Y.V.FALETROV, AUTHOR 2 K.M.BOYKO,N.N.SLUCHANKO REVDAT 3 07-FEB-24 8AAQ 1 REMARK REVDAT 2 30-AUG-23 8AAQ 1 JRNL REVDAT 1 01-FEB-23 8AAQ 0 JRNL AUTH L.A.VARFOLOMEEVA,Y.B.SLONIMSKIY,N.A.EGORKIN,M.E.MINYAEV, JRNL AUTH 2 Y.V.FALETROV,K.M.BOYKO,N.N.SLUCHANKO JRNL TITL PREPARATION AND STRUCTURAL STUDIES OF THE SILKWORM JRNL TITL 2 CAROTENOID-BINDING PROTEIN COMPLEXED WITH A NEW PIGMENT JRNL REF CRYSTALLOGRAPHY REPORTS 2022 JRNL REFN ISSN 1063-7745 JRNL DOI 10.1134/S1063774522060281 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 21421 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1104 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1200 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 73.29 REMARK 3 BIN R VALUE (WORKING SET) : 0.3110 REMARK 3 BIN FREE R VALUE SET COUNT : 51 REMARK 3 BIN FREE R VALUE : 0.3830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : -0.19000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.284 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1855 ; 0.018 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2520 ; 2.544 ; 1.638 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 228 ; 7.496 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 97 ;30.541 ;21.237 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 309 ;15.204 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;18.712 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 241 ; 0.169 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1406 ; 0.017 ; 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): 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 : 1 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 67 A 297 REMARK 3 ORIGIN FOR THE GROUP (A): 16.0941 12.7887 -17.2916 REMARK 3 T TENSOR REMARK 3 T11: 0.0075 T22: 0.0055 REMARK 3 T33: 0.0097 T12: 0.0040 REMARK 3 T13: 0.0067 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.4533 L22: 0.8796 REMARK 3 L33: 0.8847 L12: -0.0172 REMARK 3 L13: 0.1024 L23: -0.0309 REMARK 3 S TENSOR REMARK 3 S11: -0.0037 S12: -0.0364 S13: -0.0033 REMARK 3 S21: 0.0004 S22: -0.0057 S23: 0.0493 REMARK 3 S31: 0.0278 S32: 0.0219 S33: 0.0095 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: U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 8AAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292124111. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-6000HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22589 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.90900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 7ZTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, 0.1 M BIS-TRIS PROPANE PH 7.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 60.13100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.13100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.05950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.22250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.05950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.22250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.13100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.05950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.22250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 60.13100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.05950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.22250 REMARK 290 SMTRY3 8 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 HOH A 352 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 431 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 441 LIES ON A SPECIAL POSITION. 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 45 REMARK 465 GLY A 46 REMARK 465 SER A 47 REMARK 465 SER A 48 REMARK 465 HIS A 49 REMARK 465 HIS A 50 REMARK 465 HIS A 51 REMARK 465 HIS A 52 REMARK 465 HIS A 53 REMARK 465 HIS A 54 REMARK 465 SER A 55 REMARK 465 SER A 56 REMARK 465 GLY A 57 REMARK 465 LEU A 58 REMARK 465 GLU A 59 REMARK 465 VAL A 60 REMARK 465 LEU A 61 REMARK 465 PHE A 62 REMARK 465 GLN A 63 REMARK 465 GLY A 64 REMARK 465 PRO A 65 REMARK 465 HIS A 66 REMARK 465 GLY A 172 REMARK 465 LYS A 261 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 MET A 67 CG SD CE REMARK 470 ARG A 179 NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 111 CG CD OE1 OE2 REMARK 480 LYS A 140 CD CE NZ REMARK 480 ARG A 195 NE CZ NH1 NH2 REMARK 480 ASN A 200 CB CG OD1 ND2 REMARK 480 LYS A 220 CD CE NZ REMARK 480 LYS A 245 CG CD CE NZ REMARK 480 LYS A 263 CG CD CE NZ 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 GLU A 193 CD GLU A 193 OE1 0.095 REMARK 500 ARG A 195 CD ARG A 195 NE 0.186 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 97 CB - CG - CD ANGL. DEV. = 17.2 DEGREES REMARK 500 ARG A 108 CB - CG - CD ANGL. DEV. = -19.5 DEGREES REMARK 500 ARG A 128 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 128 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 128 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 173 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 195 CG - CD - NE ANGL. DEV. = -12.8 DEGREES REMARK 500 TYR A 233 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 LYS A 263 CA - CB - CG ANGL. DEV. = 15.4 DEGREES REMARK 500 ARG A 294 CB - CG - CD ANGL. DEV. = 21.4 DEGREES REMARK 500 ARG A 294 CG - CD - NE ANGL. DEV. = -18.6 DEGREES REMARK 500 ARG A 294 NE - CZ - NH2 ANGL. DEV. = -3.4 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 91 77.46 72.03 REMARK 500 ASN A 200 57.01 37.78 REMARK 500 PRO A 214 -61.73 -27.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 258 ASP A 259 145.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 8AAQ A 68 297 UNP Q8MYA9 Q8MYA9_BOMMO 68 297 SEQADV 8AAQ MET A 45 UNP Q8MYA9 INITIATING METHIONINE SEQADV 8AAQ GLY A 46 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ SER A 47 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ SER A 48 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 49 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 50 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 51 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 52 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 53 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 54 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ SER A 55 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ SER A 56 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ GLY A 57 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ LEU A 58 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ GLU A 59 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ VAL A 60 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ LEU A 61 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ PHE A 62 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ GLN A 63 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ GLY A 64 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ PRO A 65 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ HIS A 66 UNP Q8MYA9 EXPRESSION TAG SEQADV 8AAQ MET A 67 UNP Q8MYA9 EXPRESSION TAG SEQRES 1 A 253 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 253 LEU GLU VAL LEU PHE GLN GLY PRO HIS MET SER ILE ASP SEQRES 3 A 253 GLU TYR LYS SER GLN ALA ASN GLU SER MET ALA ASN ALA SEQRES 4 A 253 TRP ARG ILE ILE THR LEU PRO ASN TRP THR VAL GLU LYS SEQRES 5 A 253 ARG GLY THR VAL ARG GLY ASP VAL VAL GLU SER ARG LYS SEQRES 6 A 253 VAL GLU GLY PHE GLY LYS VAL TYR ARG PHE THR GLY VAL SEQRES 7 A 253 VAL ASN CYS PRO ALA ARG PHE LEU TYR GLU GLU PHE LYS SEQRES 8 A 253 ASN ASN LEU THR LYS LEU PRO GLU TRP ASN PRO THR ILE SEQRES 9 A 253 LEU LYS CYS GLU ILE ILE LYS GLU ILE GLY ASP GLY VAL SEQRES 10 A 253 ASP LEU SER TYR GLN VAL THR ALA GLY GLY GLY ARG GLY SEQRES 11 A 253 ILE ILE THR PRO ARG ASP PHE VAL ILE LEU ARG ARG THR SEQRES 12 A 253 ALA LEU LEU SER ARG GLU GLY ARG VAL VAL ASP ASP ASN SEQRES 13 A 253 PRO HIS GLY TYR ILE SER SER GLY VAL SER VAL GLN VAL SEQRES 14 A 253 PRO GLY TYR PRO PRO LEU LYS GLU MET VAL ARG GLY HIS SEQRES 15 A 253 ASN LYS VAL GLY CYS TRP TYR LEU GLN PRO ARG THR VAL SEQRES 16 A 253 GLN THR PRO GLY GLY LYS ILE GLU ASP GLN ALA LEU PHE SEQRES 17 A 253 GLN TRP LEU MET CYS CYS ASP LEU LYS GLY LYS ILE PRO SEQRES 18 A 253 GLN PHE VAL LEU ASP VAL ALA PHE ALA THR VAL MET LEU SEQRES 19 A 253 ASP TYR ILE VAL HIS VAL ARG LYS PHE VAL ALA GLU ALA SEQRES 20 A 253 LYS ALA ARG ALA GLU ILE FORMUL 2 HOH *162(H2 O) HELIX 1 AA1 SER A 68 THR A 88 1 21 HELIX 2 AA2 PRO A 126 ASN A 137 1 12 HELIX 3 AA3 LYS A 140 ASN A 145 1 6 HELIX 4 AA4 PRO A 265 ARG A 294 1 30 SHEET 1 AA1 8 THR A 93 ARG A 97 0 SHEET 2 AA1 8 VAL A 104 VAL A 110 -1 O VAL A 105 N GLU A 95 SHEET 3 AA1 8 GLY A 114 VAL A 123 -1 O ARG A 118 N GLU A 106 SHEET 4 AA1 8 ILE A 246 ASP A 259 -1 O PHE A 252 N GLY A 121 SHEET 5 AA1 8 HIS A 226 GLN A 240 -1 N GLN A 235 O LEU A 251 SHEET 6 AA1 8 GLY A 203 SER A 210 -1 N SER A 210 O ASN A 227 SHEET 7 AA1 8 ARG A 179 LEU A 190 -1 N LEU A 184 O VAL A 209 SHEET 8 AA1 8 VAL A 196 VAL A 197 -1 O VAL A 197 N LEU A 189 SHEET 1 AA2 4 ILE A 148 GLY A 158 0 SHEET 2 AA2 4 VAL A 161 THR A 168 -1 O TYR A 165 N GLU A 152 SHEET 3 AA2 4 ARG A 179 LEU A 190 -1 O ARG A 179 N THR A 168 SHEET 4 AA2 4 VAL A 223 ARG A 224 1 O VAL A 223 N ASP A 180 CRYST1 62.119 66.445 120.262 90.00 90.00 90.00 C 2 2 21 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 0.016098 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008315 0.00000