PDB Short entry for 1SVD HEADER LYASE 29-MAR-04 1SVD TITLE THE STRUCTURE OF HALOTHIOBACILLUS NEAPOLITANUS RUBISCO COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE COMPND 3 SUBUNIT; COMPND 4 CHAIN: A; COMPND 5 EC: 4.1.1.39; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN; COMPND 8 CHAIN: M; COMPND 9 SYNONYM: RUBISCO SMALL SUBUNIT; COMPND 10 EC: 4.1.1.39 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HALOTHIOBACILLUS NEAPOLITANUS; SOURCE 3 ORGANISM_TAXID: 927; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HALOTHIOBACILLUS NEAPOLITANUS; SOURCE 6 ORGANISM_TAXID: 927 KEYWDS BETA-ALPHA-BARREL, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.KERFELD,M.R.SAWAYA,I.PASHKOV,G.CANNON,E.WILLIAMS,K.TRAN, AUTHOR 2 T.O.YEATES REVDAT 4 23-AUG-23 1SVD 1 REMARK REVDAT 3 13-JUL-11 1SVD 1 VERSN REVDAT 2 24-FEB-09 1SVD 1 VERSN REVDAT 1 12-APR-05 1SVD 0 JRNL AUTH C.A.KERFELD,M.R.SAWAYA,I.PASHKOV,G.CANNON,E.WILLIAMS,K.TRAN, JRNL AUTH 2 T.O.YEATES JRNL TITL THE STRUCTURE OF HALOTHIOBACILLUS NEAPOLITANUS RUBISCO JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 87.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 58984 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) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3095 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) : 4304 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1620 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.1980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4369 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -0.98000 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): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.086 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.538 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.956 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4544 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 4008 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6169 ; 1.519 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9305 ; 0.910 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 5.893 ; 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): 643 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5150 ; 0.015 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 984 ; 0.022 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 881 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4649 ; 0.246 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2571 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 302 ; 0.124 ; 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): 45 ; 0.223 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 137 ; 0.304 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 40 ; 0.307 ; 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): 2764 ; 0.945 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4432 ; 1.759 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1780 ; 2.665 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1737 ; 4.207 ; 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 16 A 460 REMARK 3 ORIGIN FOR THE GROUP (A): 19.6543 30.1686 12.6002 REMARK 3 T TENSOR REMARK 3 T11: 0.0268 T22: 0.0381 REMARK 3 T33: 0.0593 T12: -0.0179 REMARK 3 T13: 0.0012 T23: -0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.0958 L22: 0.2307 REMARK 3 L33: 0.2864 L12: -0.0846 REMARK 3 L13: 0.0587 L23: -0.1110 REMARK 3 S TENSOR REMARK 3 S11: -0.0113 S12: -0.0012 S13: 0.0485 REMARK 3 S21: 0.0068 S22: -0.0080 S23: -0.0588 REMARK 3 S31: -0.0251 S32: 0.0371 S33: 0.0192 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 : M 3 M 110 REMARK 3 ORIGIN FOR THE GROUP (A): 3.6119 29.6921 41.0339 REMARK 3 T TENSOR REMARK 3 T11: 0.0550 T22: 0.0606 REMARK 3 T33: 0.0131 T12: 0.0010 REMARK 3 T13: 0.0099 T23: -0.0217 REMARK 3 L TENSOR REMARK 3 L11: 0.4816 L22: 0.3182 REMARK 3 L33: 0.1755 L12: 0.1617 REMARK 3 L13: 0.2305 L23: 0.1629 REMARK 3 S TENSOR REMARK 3 S11: 0.0296 S12: -0.1076 S13: 0.0532 REMARK 3 S21: 0.0481 S22: -0.0370 S23: 0.0341 REMARK 3 S31: -0.0184 S32: -0.0468 S33: 0.0073 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 1SVD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-04. REMARK 100 THE DEPOSITION ID IS D_1000022024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : DOUBLE CRYSTAL SI(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.4000 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) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 1RBL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, CITRATE, COBALT REMARK 280 CHLORIDE, GLYCEROL, PH 5.8, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 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,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 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 SMTRY1 9 1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 78.53300 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 53.80450 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 78.53300 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 53.80450 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 78.53300 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 53.80450 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 78.53300 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 53.80450 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 78.53300 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 53.80450 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 78.53300 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 53.80450 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 78.53300 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 53.80450 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 78.53300 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 78.53300 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 53.80450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS AN L(8)S(8) OCTAMER GENERATED REMARK 300 FROM THE LARGE(L) AND SMALL (S) SUBNITS IN THE ASYMMETRIC UNIT BY REMARK 300 THE OPERATIONS: X,Y,Z; -X,-Y,Z; -Y,X,Z; Y,-X,Z; -X,Y,-Z; X,-Y,-Z; Y, REMARK 300 X,-Z; -Y,-X,-Z. 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXADECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 84410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 129540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -520.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M 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 0.00000 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 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 6 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 7 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 7 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, M 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 0.00000 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 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 681 LIES ON A SPECIAL POSITION. REMARK 375 HOH M 170 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 1 REMARK 465 ALA A 2 REMARK 465 VAL A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 TYR A 6 REMARK 465 SER A 7 REMARK 465 ALA A 8 REMARK 465 GLY A 9 REMARK 465 VAL A 10 REMARK 465 LYS A 11 REMARK 465 GLU A 12 REMARK 465 TYR A 13 REMARK 465 ARG A 14 REMARK 465 GLN A 15 REMARK 465 GLU A 461 REMARK 465 PHE A 462 REMARK 465 ASP A 463 REMARK 465 THR A 464 REMARK 465 VAL A 465 REMARK 465 ASP A 466 REMARK 465 LYS A 467 REMARK 465 LEU A 468 REMARK 465 ASP A 469 REMARK 465 THR A 470 REMARK 465 GLN A 471 REMARK 465 ASN A 472 REMARK 465 ARG A 473 REMARK 465 MET M 1 REMARK 465 ALA M 2 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 ASN M 110 CB CG OD1 ND2 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 OD1 ASP A 196 ND2 ASN A 198 2.13 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 187 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 209 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 331 CB - CG - OD2 ANGL. DEV. = 5.9 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 55 -70.32 -137.45 REMARK 500 HIS A 146 -52.71 -128.75 REMARK 500 ASN A 200 -84.90 -125.64 REMARK 500 MET A 205 93.01 -162.45 REMARK 500 MET A 290 -1.09 80.02 REMARK 500 VAL A 324 -51.53 69.23 REMARK 500 ASP A 350 94.47 -160.41 REMARK 500 TYR M 13 33.58 -143.24 REMARK 500 GLU M 14 -146.52 67.48 REMARK 500 PHE M 16 -1.77 78.22 REMARK 500 LYS M 60 -130.81 54.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 474 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 475 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL M 111 DBREF 1SVD A 1 473 UNP O85040 O85040_THINE 1 473 DBREF 1SVD M 1 110 UNP P45686 RBS_THINE 1 110 SEQRES 1 A 473 MET ALA VAL LYS LYS TYR SER ALA GLY VAL LYS GLU TYR SEQRES 2 A 473 ARG GLN THR TYR TRP MET PRO GLU TYR THR PRO LEU ASP SEQRES 3 A 473 SER ASP ILE LEU ALA CYS PHE LYS ILE THR PRO GLN PRO SEQRES 4 A 473 GLY VAL ASP ARG GLU GLU ALA ALA ALA ALA VAL ALA ALA SEQRES 5 A 473 GLU SER SER THR GLY THR TRP THR THR VAL TRP THR ASP SEQRES 6 A 473 LEU LEU THR ASP MET ASP TYR TYR LYS GLY ARG ALA TYR SEQRES 7 A 473 ARG ILE GLU ASP VAL PRO GLY ASP ASP ALA ALA PHE TYR SEQRES 8 A 473 ALA PHE ILE ALA TYR PRO ILE ASP LEU PHE GLU GLU GLY SEQRES 9 A 473 SER VAL VAL ASN VAL PHE THR SER LEU VAL GLY ASN VAL SEQRES 10 A 473 PHE GLY PHE LYS ALA VAL ARG GLY LEU ARG LEU GLU ASP SEQRES 11 A 473 VAL ARG PHE PRO LEU ALA TYR VAL LYS THR CYS GLY GLY SEQRES 12 A 473 PRO PRO HIS GLY ILE GLN VAL GLU ARG ASP LYS MET ASN SEQRES 13 A 473 LYS TYR GLY ARG PRO LEU LEU GLY CYS THR ILE LYS PRO SEQRES 14 A 473 LYS LEU GLY LEU SER ALA LYS ASN TYR GLY ARG ALA VAL SEQRES 15 A 473 TYR GLU CYS LEU ARG GLY GLY LEU ASP PHE THR LYS ASP SEQRES 16 A 473 ASP GLU ASN ILE ASN SER GLN PRO PHE MET ARG TRP ARG SEQRES 17 A 473 ASP ARG PHE LEU PHE VAL GLN ASP ALA THR GLU THR ALA SEQRES 18 A 473 GLU ALA GLN THR GLY GLU ARG LYS GLY HIS TYR LEU ASN SEQRES 19 A 473 VAL THR ALA PRO THR PRO GLU GLU MET TYR LYS ARG ALA SEQRES 20 A 473 GLU PHE ALA LYS GLU ILE GLY ALA PRO ILE ILE MET HIS SEQRES 21 A 473 ASP TYR ILE THR GLY GLY PHE THR ALA ASN THR GLY LEU SEQRES 22 A 473 ALA LYS TRP CYS GLN ASP ASN GLY VAL LEU LEU HIS ILE SEQRES 23 A 473 HIS ARG ALA MET HIS ALA VAL ILE ASP ARG ASN PRO ASN SEQRES 24 A 473 HIS GLY ILE HIS PHE ARG VAL LEU THR LYS ILE LEU ARG SEQRES 25 A 473 LEU SER GLY GLY ASP HIS LEU HIS THR GLY THR VAL VAL SEQRES 26 A 473 GLY LYS LEU GLU GLY ASP ARG ALA SER THR LEU GLY TRP SEQRES 27 A 473 ILE ASP LEU LEU ARG GLU SER PHE ILE PRO GLU ASP ARG SEQRES 28 A 473 SER ARG GLY ILE PHE PHE ASP GLN ASP TRP GLY SER MET SEQRES 29 A 473 PRO GLY VAL PHE ALA VAL ALA SER GLY GLY ILE HIS VAL SEQRES 30 A 473 TRP HIS MET PRO ALA LEU VAL ASN ILE PHE GLY ASP ASP SEQRES 31 A 473 SER VAL LEU GLN PHE GLY GLY GLY THR LEU GLY HIS PRO SEQRES 32 A 473 TRP GLY ASN ALA ALA GLY ALA ALA ALA ASN ARG VAL ALA SEQRES 33 A 473 LEU GLU ALA CYS VAL GLU ALA ARG ASN GLN GLY ARG ASP SEQRES 34 A 473 ILE GLU LYS GLU GLY LYS GLU ILE LEU THR ALA ALA ALA SEQRES 35 A 473 GLN HIS SER PRO GLU LEU LYS ILE ALA MET GLU THR TRP SEQRES 36 A 473 LYS GLU ILE LYS PHE GLU PHE ASP THR VAL ASP LYS LEU SEQRES 37 A 473 ASP THR GLN ASN ARG SEQRES 1 M 110 MET ALA GLU MET GLN ASP TYR LYS GLN SER LEU LYS TYR SEQRES 2 M 110 GLU THR PHE SER TYR LEU PRO PRO MET ASN ALA GLU ARG SEQRES 3 M 110 ILE ARG ALA GLN ILE LYS TYR ALA ILE ALA GLN GLY TRP SEQRES 4 M 110 SER PRO GLY ILE GLU HIS VAL GLU VAL LYS ASN SER MET SEQRES 5 M 110 ASN GLN TYR TRP TYR MET TRP LYS LEU PRO PHE PHE GLY SEQRES 6 M 110 GLU GLN ASN VAL ASP ASN VAL LEU ALA GLU ILE GLU ALA SEQRES 7 M 110 CYS ARG SER ALA TYR PRO THR HIS GLN VAL LYS LEU VAL SEQRES 8 M 110 ALA TYR ASP ASN TYR ALA GLN SER LEU GLY LEU ALA PHE SEQRES 9 M 110 VAL VAL TYR ARG GLY ASN HET SO4 A 474 5 HET SO4 A 475 5 HET GOL M 111 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *354(H2 O) HELIX 1 1 ASP A 42 SER A 54 1 13 HELIX 2 2 VAL A 62 THR A 68 5 7 HELIX 3 3 PRO A 97 PHE A 101 5 5 HELIX 4 4 SER A 105 GLY A 115 1 11 HELIX 5 5 ASN A 116 PHE A 120 5 5 HELIX 6 6 PRO A 134 LYS A 139 1 6 HELIX 7 7 GLY A 147 ASN A 156 1 10 HELIX 8 8 SER A 174 GLY A 188 1 15 HELIX 9 9 ARG A 206 GLY A 226 1 21 HELIX 10 10 THR A 239 GLY A 254 1 16 HELIX 11 11 GLY A 266 GLY A 281 1 16 HELIX 12 12 MET A 290 ARG A 296 1 7 HELIX 13 13 HIS A 303 GLY A 315 1 13 HELIX 14 14 LEU A 328 ASP A 331 5 4 HELIX 15 15 ARG A 332 GLU A 344 1 13 HELIX 16 16 ASP A 350 GLY A 354 5 5 HELIX 17 17 HIS A 376 TRP A 378 5 3 HELIX 18 18 HIS A 379 GLY A 388 1 10 HELIX 19 19 GLY A 396 GLY A 401 1 6 HELIX 20 20 GLY A 405 GLN A 426 1 22 HELIX 21 21 GLU A 433 GLN A 443 1 11 HELIX 22 22 SER A 445 LYS A 456 1 12 HELIX 23 23 ASN M 23 GLN M 37 1 15 HELIX 24 24 GLU M 47 SER M 51 5 5 HELIX 25 25 ASN M 68 TYR M 83 1 16 SHEET 1 A 5 ARG A 76 VAL A 83 0 SHEET 2 A 5 ASP A 86 TYR A 96 -1 O TYR A 91 N GLU A 81 SHEET 3 A 5 ILE A 29 PRO A 37 -1 N ILE A 35 O PHE A 90 SHEET 4 A 5 VAL A 123 ARG A 132 -1 O ARG A 127 N LYS A 34 SHEET 5 A 5 GLY A 301 ILE A 302 1 O GLY A 301 N LEU A 126 SHEET 1 B 9 LEU A 162 THR A 166 0 SHEET 2 B 9 PHE A 192 LYS A 194 1 O PHE A 192 N LEU A 163 SHEET 3 B 9 GLY A 230 ASN A 234 1 O TYR A 232 N THR A 193 SHEET 4 B 9 ILE A 257 ASP A 261 1 O MET A 259 N LEU A 233 SHEET 5 B 9 LEU A 283 HIS A 287 1 O HIS A 285 N ILE A 258 SHEET 6 B 9 HIS A 318 HIS A 320 1 O HIS A 318 N ILE A 286 SHEET 7 B 9 PHE A 368 SER A 372 1 O VAL A 370 N LEU A 319 SHEET 8 B 9 SER A 391 GLN A 394 1 O GLN A 394 N ALA A 371 SHEET 9 B 9 LEU A 162 THR A 166 1 N LEU A 162 O LEU A 393 SHEET 1 C 2 PHE A 346 ILE A 347 0 SHEET 2 C 2 GLN A 359 ASP A 360 -1 O GLN A 359 N ILE A 347 SHEET 1 D 4 TYR M 57 TRP M 59 0 SHEET 2 D 4 SER M 40 VAL M 46 -1 N ILE M 43 O TRP M 59 SHEET 3 D 4 GLN M 87 ASP M 94 -1 O LYS M 89 N GLU M 44 SHEET 4 D 4 SER M 99 TYR M 107 -1 O SER M 99 N ASP M 94 CISPEP 1 LYS A 168 PRO A 169 0 0.62 SITE 1 AC1 7 ARG A 288 HIS A 320 SER A 372 HOH A 555 SITE 2 AC1 7 HOH A 573 HOH A 646 HOH A 725 SITE 1 AC2 5 GLY A 374 GLY A 396 GLY A 397 HOH A 527 SITE 2 AC2 5 HOH A 572 SITE 1 AC3 7 ASN A 156 HOH A 642 HOH A 704 TYR M 13 SITE 2 AC3 7 SER M 51 LYS M 89 HOH M 135 CRYST1 157.066 157.066 107.609 90.00 90.00 90.00 I 4 2 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 0.006367 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006367 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009293 0.00000