HEADER LYASE 27-JUN-05 2CWX TITLE CRYSTAL STRUCTURE OF OCTAMERIC RIBULOSE-1,5-BISPHOSPHATE TITLE 2 CARBOXYLASE/OXYGENASE (RUBISCO) FROM PYROCOCCUS HORIKOSHII OT3 (FORM- TITLE 3 1 CRYSTAL) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBULOSE BISPHOSPHATE CARBOXYLASE; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, RUBISCO; COMPND 5 EC: 4.1.1.39; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS LYASE, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,C.MISHIMA,R.AKASAKA,H.UDA,T.TERADA,M.SHIROUZU,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 13-MAR-24 2CWX 1 REMARK REVDAT 3 13-JUL-11 2CWX 1 VERSN REVDAT 2 24-FEB-09 2CWX 1 VERSN REVDAT 1 27-DEC-05 2CWX 0 JRNL AUTH E.MIZOHATA,C.MISHIMA,R.AKASAKA,H.UDA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF OCTAMERIC RIBULOSE-1,5-BISPHOSPHATE JRNL TITL 2 CARBOXYLASE/OXYGENASE (RUBISCO) FROM PYROCOCCUS HORIKOSHII JRNL TITL 3 OT3 (FORM-1 CRYSTAL) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 68293 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3636 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4968 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 260 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6493 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 469 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.12000 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): 0.149 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.137 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.098 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.559 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6648 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 6124 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8979 ; 1.494 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14218 ; 0.863 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 819 ; 6.544 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 952 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7403 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1394 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1428 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 7247 ; 0.238 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3914 ; 0.087 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 284 ; 0.191 ; 0.200 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): 19 ; 0.304 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 89 ; 0.334 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.223 ; 0.200 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): 4071 ; 0.919 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6516 ; 1.789 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2577 ; 2.763 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2463 ; 4.679 ; 4.500 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 : 2 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 8 A 424 REMARK 3 ORIGIN FOR THE GROUP (A): 65.2012 35.0383 41.5877 REMARK 3 T TENSOR REMARK 3 T11: 0.0815 T22: 0.0359 REMARK 3 T33: 0.1138 T12: -0.0117 REMARK 3 T13: -0.0464 T23: -0.0139 REMARK 3 L TENSOR REMARK 3 L11: 0.8727 L22: 0.2819 REMARK 3 L33: 0.6440 L12: 0.2875 REMARK 3 L13: 0.1888 L23: 0.2690 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: -0.1140 S13: 0.1628 REMARK 3 S21: -0.0078 S22: -0.0888 S23: 0.0663 REMARK 3 S31: -0.0764 S32: 0.0057 S33: 0.1113 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 : E 10 E 417 REMARK 3 ORIGIN FOR THE GROUP (A): 74.7895 35.1123 16.0648 REMARK 3 T TENSOR REMARK 3 T11: 0.1090 T22: 0.0541 REMARK 3 T33: 0.0875 T12: -0.0017 REMARK 3 T13: -0.0451 T23: 0.0559 REMARK 3 L TENSOR REMARK 3 L11: 0.9801 L22: 0.4031 REMARK 3 L33: 0.6194 L12: 0.3520 REMARK 3 L13: 0.0502 L23: 0.1316 REMARK 3 S TENSOR REMARK 3 S11: -0.0482 S12: 0.1829 S13: 0.1670 REMARK 3 S21: -0.0681 S22: 0.0210 S23: 0.0315 REMARK 3 S31: -0.0849 S32: -0.0065 S33: 0.0272 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2CWX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024718. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71958 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NACL, PEG6000, TRIS, PH 8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 2 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 71.99600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 71.99600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 71.99600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 71.99600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 71.99600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.99600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 71.99600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.99600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 143.99200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 -1.000000 0.000000 71.99600 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 -71.99600 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 71.99600 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 71.99600 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 1 REMARK 465 MET A 2 REMARK 465 VAL A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 MET A 6 REMARK 465 LYS A 7 REMARK 465 TRP A 55 REMARK 465 THR A 56 REMARK 465 THR A 57 REMARK 465 LYS A 425 REMARK 465 VAL A 426 REMARK 465 GLY A 427 REMARK 465 VAL A 428 REMARK 465 GLN A 429 REMARK 465 HIS A 430 REMARK 465 MET E 1 REMARK 465 MET E 2 REMARK 465 VAL E 3 REMARK 465 LEU E 4 REMARK 465 ARG E 5 REMARK 465 MET E 6 REMARK 465 LYS E 7 REMARK 465 VAL E 8 REMARK 465 GLU E 9 REMARK 465 GLU E 418 REMARK 465 VAL E 419 REMARK 465 GLY E 420 REMARK 465 LEU E 421 REMARK 465 SER E 422 REMARK 465 LYS E 423 REMARK 465 ALA E 424 REMARK 465 LYS E 425 REMARK 465 VAL E 426 REMARK 465 GLY E 427 REMARK 465 VAL E 428 REMARK 465 GLN E 429 REMARK 465 HIS E 430 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 ALA A 424 O 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 O GLU E 95 O HOH E 585 2.11 REMARK 500 O GLU E 63 O HOH E 535 2.14 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 E 609 O HOH E 651 4555 2.17 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 GLU A 266 CD GLU A 266 OE1 0.072 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 ASP A 151 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 VAL A 231 CB - CA - C ANGL. DEV. = -11.5 DEGREES REMARK 500 ASP A 331 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP E 16 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP E 391 CB - CG - OD2 ANGL. DEV. = 5.7 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 SER A 51 -108.92 -127.17 REMARK 500 LEU A 61 104.00 -56.71 REMARK 500 THR A 192 -81.54 -106.87 REMARK 500 ASN A 197 81.42 -157.28 REMARK 500 MET A 281 -14.13 88.54 REMARK 500 LYS A 318 -73.21 -46.20 REMARK 500 TRP A 337 73.06 -152.53 REMARK 500 GLU A 338 -132.76 56.82 REMARK 500 SER E 51 -109.84 -133.65 REMARK 500 TRP E 55 135.29 169.55 REMARK 500 THR E 56 23.15 -145.01 REMARK 500 THR E 57 -87.54 -73.16 REMARK 500 TRP E 59 67.61 66.94 REMARK 500 LYS E 60 106.03 44.04 REMARK 500 ASP E 151 -54.87 -124.32 REMARK 500 THR E 192 -79.71 -111.12 REMARK 500 ASN E 197 77.78 -158.01 REMARK 500 MET E 281 -16.54 90.38 REMARK 500 VAL E 316 -137.72 -151.28 REMARK 500 ALA E 320 -94.56 63.36 REMARK 500 TRP E 337 78.76 -152.62 REMARK 500 GLU E 338 -122.04 46.95 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 THR E 54 TRP E 55 142.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CXE RELATED DB: PDB REMARK 900 FORM-2 CRYSTAL REMARK 900 RELATED ID: PHO001000939.2 RELATED DB: TARGETDB DBREF 2CWX A 1 430 UNP O58677 RBL_PYRHO 1 430 DBREF 2CWX E 1 430 UNP O58677 RBL_PYRHO 1 430 SEQRES 1 A 430 MET MET VAL LEU ARG MET LYS VAL GLU TRP TYR LEU ASP SEQRES 2 A 430 PHE VAL ASP LEU ASN TYR GLU PRO GLY ARG ASP GLU LEU SEQRES 3 A 430 ILE VAL GLU TYR TYR PHE GLU PRO ASN GLY VAL SER PRO SEQRES 4 A 430 GLU GLU ALA ALA GLY ARG ILE ALA SER GLU SER SER ILE SEQRES 5 A 430 GLY THR TRP THR THR LEU TRP LYS LEU PRO GLU MET ALA SEQRES 6 A 430 LYS ARG SER MET ALA LYS VAL PHE TYR LEU GLU LYS HIS SEQRES 7 A 430 GLY GLU GLY TYR ILE ALA LYS ILE ALA TYR PRO LEU THR SEQRES 8 A 430 LEU PHE GLU GLU GLY SER LEU VAL GLN LEU PHE SER ALA SEQRES 9 A 430 VAL ALA GLY ASN VAL PHE GLY MET LYS ALA LEU LYS ASN SEQRES 10 A 430 LEU ARG LEU LEU ASP PHE HIS PRO PRO TYR GLU TYR LEU SEQRES 11 A 430 ARG HIS PHE LYS GLY PRO GLN PHE GLY VAL GLN GLY ILE SEQRES 12 A 430 ARG GLU PHE MET GLY VAL LYS ASP ARG PRO LEU THR ALA SEQRES 13 A 430 THR VAL PRO LYS PRO LYS MET GLY TRP SER VAL GLU GLU SEQRES 14 A 430 TYR ALA GLU ILE ALA TYR GLU LEU TRP SER GLY GLY ILE SEQRES 15 A 430 ASP LEU LEU LYS ASP ASP GLU ASN PHE THR SER PHE PRO SEQRES 16 A 430 PHE ASN ARG PHE GLU GLU ARG VAL ARG LYS LEU TYR ARG SEQRES 17 A 430 VAL ARG ASP ARG VAL GLU ALA GLU THR GLY GLU THR LYS SEQRES 18 A 430 GLU TYR LEU ILE ASN ILE THR GLY PRO VAL ASN ILE MET SEQRES 19 A 430 GLU LYS ARG ALA GLU MET VAL ALA ASN GLU GLY GLY GLN SEQRES 20 A 430 TYR VAL MET ILE ASP ILE VAL VAL ALA GLY TRP SER ALA SEQRES 21 A 430 LEU GLN TYR MET ARG GLU VAL THR GLU ASP LEU GLY LEU SEQRES 22 A 430 ALA ILE HIS ALA HIS ARG ALA MET HIS ALA ALA PHE THR SEQRES 23 A 430 ARG ASN PRO ARG HIS GLY ILE THR MET LEU ALA LEU ALA SEQRES 24 A 430 LYS ALA ALA ARG MET ILE GLY VAL ASP GLN ILE HIS THR SEQRES 25 A 430 GLY THR ALA VAL GLY LYS MET ALA GLY ASN TYR GLU GLU SEQRES 26 A 430 ILE LYS ARG ILE ASN ASP PHE LEU LEU SER LYS TRP GLU SEQRES 27 A 430 HIS ILE ARG PRO VAL PHE PRO VAL ALA SER GLY GLY LEU SEQRES 28 A 430 HIS PRO GLY LEU MET PRO GLU LEU ILE ARG LEU PHE GLY SEQRES 29 A 430 LYS ASP LEU VAL ILE GLN ALA GLY GLY GLY VAL MET GLY SEQRES 30 A 430 HIS PRO ASP GLY PRO ARG ALA GLY ALA LYS ALA LEU ARG SEQRES 31 A 430 ASP ALA ILE ASP ALA ALA ILE GLU GLY VAL ASP LEU ASP SEQRES 32 A 430 GLU LYS ALA LYS SER SER PRO GLU LEU LYS LYS SER LEU SEQRES 33 A 430 ARG GLU VAL GLY LEU SER LYS ALA LYS VAL GLY VAL GLN SEQRES 34 A 430 HIS SEQRES 1 E 430 MET MET VAL LEU ARG MET LYS VAL GLU TRP TYR LEU ASP SEQRES 2 E 430 PHE VAL ASP LEU ASN TYR GLU PRO GLY ARG ASP GLU LEU SEQRES 3 E 430 ILE VAL GLU TYR TYR PHE GLU PRO ASN GLY VAL SER PRO SEQRES 4 E 430 GLU GLU ALA ALA GLY ARG ILE ALA SER GLU SER SER ILE SEQRES 5 E 430 GLY THR TRP THR THR LEU TRP LYS LEU PRO GLU MET ALA SEQRES 6 E 430 LYS ARG SER MET ALA LYS VAL PHE TYR LEU GLU LYS HIS SEQRES 7 E 430 GLY GLU GLY TYR ILE ALA LYS ILE ALA TYR PRO LEU THR SEQRES 8 E 430 LEU PHE GLU GLU GLY SER LEU VAL GLN LEU PHE SER ALA SEQRES 9 E 430 VAL ALA GLY ASN VAL PHE GLY MET LYS ALA LEU LYS ASN SEQRES 10 E 430 LEU ARG LEU LEU ASP PHE HIS PRO PRO TYR GLU TYR LEU SEQRES 11 E 430 ARG HIS PHE LYS GLY PRO GLN PHE GLY VAL GLN GLY ILE SEQRES 12 E 430 ARG GLU PHE MET GLY VAL LYS ASP ARG PRO LEU THR ALA SEQRES 13 E 430 THR VAL PRO LYS PRO LYS MET GLY TRP SER VAL GLU GLU SEQRES 14 E 430 TYR ALA GLU ILE ALA TYR GLU LEU TRP SER GLY GLY ILE SEQRES 15 E 430 ASP LEU LEU LYS ASP ASP GLU ASN PHE THR SER PHE PRO SEQRES 16 E 430 PHE ASN ARG PHE GLU GLU ARG VAL ARG LYS LEU TYR ARG SEQRES 17 E 430 VAL ARG ASP ARG VAL GLU ALA GLU THR GLY GLU THR LYS SEQRES 18 E 430 GLU TYR LEU ILE ASN ILE THR GLY PRO VAL ASN ILE MET SEQRES 19 E 430 GLU LYS ARG ALA GLU MET VAL ALA ASN GLU GLY GLY GLN SEQRES 20 E 430 TYR VAL MET ILE ASP ILE VAL VAL ALA GLY TRP SER ALA SEQRES 21 E 430 LEU GLN TYR MET ARG GLU VAL THR GLU ASP LEU GLY LEU SEQRES 22 E 430 ALA ILE HIS ALA HIS ARG ALA MET HIS ALA ALA PHE THR SEQRES 23 E 430 ARG ASN PRO ARG HIS GLY ILE THR MET LEU ALA LEU ALA SEQRES 24 E 430 LYS ALA ALA ARG MET ILE GLY VAL ASP GLN ILE HIS THR SEQRES 25 E 430 GLY THR ALA VAL GLY LYS MET ALA GLY ASN TYR GLU GLU SEQRES 26 E 430 ILE LYS ARG ILE ASN ASP PHE LEU LEU SER LYS TRP GLU SEQRES 27 E 430 HIS ILE ARG PRO VAL PHE PRO VAL ALA SER GLY GLY LEU SEQRES 28 E 430 HIS PRO GLY LEU MET PRO GLU LEU ILE ARG LEU PHE GLY SEQRES 29 E 430 LYS ASP LEU VAL ILE GLN ALA GLY GLY GLY VAL MET GLY SEQRES 30 E 430 HIS PRO ASP GLY PRO ARG ALA GLY ALA LYS ALA LEU ARG SEQRES 31 E 430 ASP ALA ILE ASP ALA ALA ILE GLU GLY VAL ASP LEU ASP SEQRES 32 E 430 GLU LYS ALA LYS SER SER PRO GLU LEU LYS LYS SER LEU SEQRES 33 E 430 ARG GLU VAL GLY LEU SER LYS ALA LYS VAL GLY VAL GLN SEQRES 34 E 430 HIS FORMUL 3 HOH *469(H2 O) HELIX 1 1 VAL A 8 ASP A 13 1 6 HELIX 2 2 SER A 38 SER A 50 1 13 HELIX 3 3 PRO A 62 SER A 68 1 7 HELIX 4 4 THR A 91 PHE A 93 5 3 HELIX 5 5 SER A 97 ALA A 106 1 10 HELIX 6 6 GLY A 107 MET A 112 5 6 HELIX 7 7 PRO A 126 ARG A 131 1 6 HELIX 8 8 PHE A 138 GLY A 148 1 11 HELIX 9 9 SER A 166 GLY A 181 1 16 HELIX 10 10 ARG A 198 GLY A 218 1 21 HELIX 11 11 PRO A 230 GLU A 244 1 15 HELIX 12 12 ILE A 253 GLY A 257 1 5 HELIX 13 13 GLY A 257 GLY A 272 1 16 HELIX 14 14 HIS A 282 ARG A 287 1 6 HELIX 15 15 THR A 294 GLY A 306 1 13 HELIX 16 16 ASN A 322 SER A 335 1 14 HELIX 17 17 HIS A 352 GLY A 354 5 3 HELIX 18 18 LEU A 355 GLY A 364 1 10 HELIX 19 19 ALA A 371 GLY A 377 1 7 HELIX 20 20 GLY A 381 GLY A 399 1 19 HELIX 21 21 ASP A 401 LYS A 407 1 7 HELIX 22 22 SER A 409 SER A 422 1 14 HELIX 23 23 TRP E 10 VAL E 15 5 6 HELIX 24 24 SER E 38 SER E 50 1 13 HELIX 25 25 ALA E 65 MET E 69 5 5 HELIX 26 26 PRO E 89 PHE E 93 5 5 HELIX 27 27 SER E 97 ALA E 106 1 10 HELIX 28 28 GLY E 107 MET E 112 5 6 HELIX 29 29 PRO E 126 ARG E 131 1 6 HELIX 30 30 PHE E 138 GLY E 148 1 11 HELIX 31 31 SER E 166 GLY E 181 1 16 HELIX 32 32 ARG E 198 GLY E 218 1 21 HELIX 33 33 PRO E 230 GLU E 244 1 15 HELIX 34 34 ILE E 253 GLY E 257 1 5 HELIX 35 35 GLY E 257 GLY E 272 1 16 HELIX 36 36 HIS E 282 ARG E 287 1 6 HELIX 37 37 THR E 294 GLY E 306 1 13 HELIX 38 38 ASN E 322 SER E 335 1 14 HELIX 39 39 HIS E 352 GLY E 354 5 3 HELIX 40 40 LEU E 355 GLY E 364 1 10 HELIX 41 41 ALA E 371 GLY E 377 1 7 HELIX 42 42 GLY E 381 GLU E 398 1 18 HELIX 43 43 ASP E 401 LYS E 407 1 7 HELIX 44 44 SER E 409 ARG E 417 1 9 SHEET 1 A 5 LYS A 71 HIS A 78 0 SHEET 2 A 5 GLY A 81 PRO A 89 -1 O ALA A 87 N LYS A 71 SHEET 3 A 5 GLU A 25 PRO A 34 -1 N LEU A 26 O TYR A 88 SHEET 4 A 5 LEU A 115 HIS A 124 -1 O LYS A 116 N GLU A 33 SHEET 5 A 5 GLY A 292 ILE A 293 1 O GLY A 292 N LEU A 120 SHEET 1 B 8 GLU A 222 LEU A 224 0 SHEET 2 B 8 LEU A 184 LYS A 186 1 N LEU A 185 O LEU A 224 SHEET 3 B 8 LEU A 154 THR A 157 1 N THR A 155 O LEU A 184 SHEET 4 B 8 VAL A 368 GLN A 370 1 O ILE A 369 N LEU A 154 SHEET 5 B 8 PHE A 344 ALA A 347 1 N ALA A 347 O GLN A 370 SHEET 6 B 8 GLN A 309 HIS A 311 1 N ILE A 310 O VAL A 346 SHEET 7 B 8 ALA A 274 HIS A 278 1 N ALA A 277 O GLN A 309 SHEET 8 B 8 TYR A 248 ASP A 252 1 N VAL A 249 O HIS A 276 SHEET 1 C 5 LYS E 71 HIS E 78 0 SHEET 2 C 5 GLY E 81 TYR E 88 -1 O GLY E 81 N HIS E 78 SHEET 3 C 5 LEU E 26 PRO E 34 -1 N LEU E 26 O TYR E 88 SHEET 4 C 5 LEU E 115 HIS E 124 -1 O ASP E 122 N GLU E 29 SHEET 5 C 5 GLY E 292 ILE E 293 1 O GLY E 292 N LEU E 120 SHEET 1 D 8 GLU E 222 LEU E 224 0 SHEET 2 D 8 LEU E 184 LYS E 186 1 N LEU E 185 O LEU E 224 SHEET 3 D 8 LEU E 154 THR E 157 1 N THR E 155 O LEU E 184 SHEET 4 D 8 VAL E 368 GLN E 370 1 O ILE E 369 N LEU E 154 SHEET 5 D 8 PHE E 344 SER E 348 1 N ALA E 347 O GLN E 370 SHEET 6 D 8 GLN E 309 HIS E 311 1 N ILE E 310 O PHE E 344 SHEET 7 D 8 ALA E 274 HIS E 278 1 N ALA E 277 O GLN E 309 SHEET 8 D 8 TYR E 248 ASP E 252 1 N VAL E 249 O HIS E 276 CISPEP 1 LYS A 160 PRO A 161 0 0.89 CISPEP 2 LYS E 160 PRO E 161 0 -3.75 CRYST1 143.992 143.992 101.417 90.00 90.00 90.00 P 4 21 2 16 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 0.006945 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006945 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009860 0.00000