HEADER LIGASE 25-MAR-16 5G1F TITLE CRYSTAL STRUCTURE OF THE 6-CARBOXYHEXANOATE-COA LIGASE (BIOW)FROM TITLE 2 BACILLUS SUBTILIS IN COMPLEX WITH COENZYME A COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-CARBOXYHEXANOATE-COA LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PIMELOYL-COA SYNTHASE, 6-CARBOXYHEXANOATE-COA LIGASE; COMPND 5 EC: 6.2.1.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.MOYNIE,M.WANG,D.J.CAMPOPIANO,J.H.NAISMITH REVDAT 3 10-JAN-24 5G1F 1 REMARK REVDAT 2 21-JUN-17 5G1F 1 ATOM REVDAT 1 08-MAR-17 5G1F 0 JRNL AUTH M.WANG,L.MOYNIE,D.J.CAMPOPIANO,J.H.NAISMITH JRNL TITL THE STRUCTURE OF THE 6-CARBOXYHEXANOATE-COA LIGASE FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30569 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1647 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2227 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.4810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.36000 REMARK 3 B22 (A**2) : -6.40000 REMARK 3 B33 (A**2) : -2.97000 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): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.193 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.237 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4131 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3877 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5572 ; 1.329 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8964 ; 0.784 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 489 ; 7.772 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;36.206 ;24.010 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;15.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;20.640 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 585 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4580 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 937 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 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 5 A 65 REMARK 3 ORIGIN FOR THE GROUP (A): 17.3225 1.9189 180.9496 REMARK 3 T TENSOR REMARK 3 T11: 0.2890 T22: 0.5610 REMARK 3 T33: 0.5249 T12: -0.0059 REMARK 3 T13: -0.1180 T23: -0.0250 REMARK 3 L TENSOR REMARK 3 L11: 6.3332 L22: 6.3296 REMARK 3 L33: 4.4154 L12: 2.2814 REMARK 3 L13: -0.2138 L23: 0.2885 REMARK 3 S TENSOR REMARK 3 S11: 0.1972 S12: -0.4119 S13: -0.3051 REMARK 3 S21: 0.7808 S22: -0.2366 S23: -0.5009 REMARK 3 S31: -0.1432 S32: 0.0862 S33: 0.0393 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 : A 66 A 184 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9415 15.0207 196.0600 REMARK 3 T TENSOR REMARK 3 T11: 0.1735 T22: 0.5048 REMARK 3 T33: 0.4691 T12: -0.0363 REMARK 3 T13: -0.0344 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.6695 L22: 3.1101 REMARK 3 L33: 4.2632 L12: -0.0284 REMARK 3 L13: -0.1379 L23: -0.1920 REMARK 3 S TENSOR REMARK 3 S11: 0.0343 S12: -0.0857 S13: -0.0233 REMARK 3 S21: 0.3089 S22: 0.0771 S23: -0.0868 REMARK 3 S31: 0.0375 S32: 0.0803 S33: -0.1115 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 185 A 256 REMARK 3 ORIGIN FOR THE GROUP (A): 19.0567 15.0344 195.6396 REMARK 3 T TENSOR REMARK 3 T11: 0.2035 T22: 0.5171 REMARK 3 T33: 0.4561 T12: -0.0256 REMARK 3 T13: -0.0371 T23: -0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.1292 L22: 3.1497 REMARK 3 L33: 4.7140 L12: -0.3879 REMARK 3 L13: 0.0828 L23: -1.3690 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: -0.0971 S13: -0.0635 REMARK 3 S21: 0.1914 S22: 0.1558 S23: -0.1018 REMARK 3 S31: 0.2432 S32: 0.1669 S33: -0.2009 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 4 B 66 REMARK 3 ORIGIN FOR THE GROUP (A): 11.7210 -3.3931 169.7179 REMARK 3 T TENSOR REMARK 3 T11: 0.0285 T22: 0.4717 REMARK 3 T33: 0.4324 T12: 0.0317 REMARK 3 T13: -0.0221 T23: -0.0371 REMARK 3 L TENSOR REMARK 3 L11: 3.6156 L22: 10.6100 REMARK 3 L33: 7.2547 L12: 2.0143 REMARK 3 L13: -0.9362 L23: -2.5093 REMARK 3 S TENSOR REMARK 3 S11: -0.0107 S12: 0.1345 S13: 0.1890 REMARK 3 S21: -0.1944 S22: 0.1093 S23: -0.1451 REMARK 3 S31: -0.3105 S32: 0.1432 S33: -0.0985 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 67 B 164 REMARK 3 ORIGIN FOR THE GROUP (A): -2.8405 -7.1574 154.9166 REMARK 3 T TENSOR REMARK 3 T11: 0.0992 T22: 0.4673 REMARK 3 T33: 0.4080 T12: -0.0393 REMARK 3 T13: 0.0224 T23: 0.0155 REMARK 3 L TENSOR REMARK 3 L11: 1.3435 L22: 4.2825 REMARK 3 L33: 2.4888 L12: -1.0775 REMARK 3 L13: 1.1133 L23: -1.3830 REMARK 3 S TENSOR REMARK 3 S11: -0.0318 S12: 0.0388 S13: -0.0070 REMARK 3 S21: -0.3742 S22: 0.1244 S23: 0.0543 REMARK 3 S31: -0.2413 S32: -0.0306 S33: -0.0927 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 165 B 258 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6727 -9.6657 156.9896 REMARK 3 T TENSOR REMARK 3 T11: 0.0052 T22: 0.4257 REMARK 3 T33: 0.3711 T12: -0.0244 REMARK 3 T13: -0.0139 T23: -0.0123 REMARK 3 L TENSOR REMARK 3 L11: 3.0622 L22: 3.6263 REMARK 3 L33: 3.7384 L12: -0.3779 REMARK 3 L13: -0.3267 L23: -0.9114 REMARK 3 S TENSOR REMARK 3 S11: 0.0002 S12: -0.0684 S13: 0.0007 REMARK 3 S21: -0.0997 S22: 0.0804 S23: -0.0516 REMARK 3 S31: -0.0204 S32: 0.0985 S33: -0.0806 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. U VALUES WITH TLS ADDED REMARK 4 REMARK 4 5G1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : XIA2, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32279 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 70.890 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : 0.76000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5FLG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG400, 0.1 M HEPES PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 25.29500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 83.21500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.18000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 83.21500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.29500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.18000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 0 REMARK 465 ALA A 1 REMARK 465 MET A 2 REMARK 465 GLU A 3 REMARK 465 GLU A 4 REMARK 465 GLY A 18 REMARK 465 SER A 19 REMARK 465 HIS A 20 REMARK 465 GLU A 21 REMARK 465 ASP A 22 REMARK 465 GLY A 23 REMARK 465 GLY A 24 REMARK 465 HIS A 257 REMARK 465 ASP A 258 REMARK 465 SER A 259 REMARK 465 GLY B 0 REMARK 465 ALA B 1 REMARK 465 MET B 2 REMARK 465 GLU B 3 REMARK 465 GLY B 18 REMARK 465 SER B 19 REMARK 465 HIS B 20 REMARK 465 GLU B 21 REMARK 465 ASP B 22 REMARK 465 GLY B 23 REMARK 465 GLY B 24 REMARK 465 SER B 259 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 GLU B 4 CG CD OE1 OE2 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 THR B 6 O HOH B 2001 2.16 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 OE1 GLU B 157 NH2 ARG B 183 4547 2.05 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 ARG A 123 46.70 -90.84 REMARK 500 LYS A 140 -120.48 48.85 REMARK 500 ILE B 27 -56.40 -120.56 REMARK 500 ARG B 123 46.40 -96.26 REMARK 500 LYS B 140 -122.94 47.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASN B 155 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 COENZYME A (COA): ONLY THE ADENOSINE 3',5'-DIPHOSPHATE REMARK 600 MOITY IS CLEARLY DEFINED IN THE ELECTRON DENSITY MAP REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 2PE A 302 REMARK 610 COA B 301 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PML A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2PE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue COA B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PML B 302 DBREF 5G1F A 4 259 UNP P53559 BIOW_BACSU 4 259 DBREF 5G1F B 4 259 UNP P53559 BIOW_BACSU 4 259 SEQADV 5G1F GLY A 0 UNP P53559 EXPRESSION TAG SEQADV 5G1F ALA A 1 UNP P53559 EXPRESSION TAG SEQADV 5G1F MET A 2 UNP P53559 EXPRESSION TAG SEQADV 5G1F GLU A 3 UNP P53559 EXPRESSION TAG SEQADV 5G1F GLY B 0 UNP P53559 EXPRESSION TAG SEQADV 5G1F ALA B 1 UNP P53559 EXPRESSION TAG SEQADV 5G1F MET B 2 UNP P53559 EXPRESSION TAG SEQADV 5G1F GLU B 3 UNP P53559 EXPRESSION TAG SEQRES 1 A 260 GLY ALA MET GLU GLU GLU THR PHE TYR SER VAL ARG MET SEQRES 2 A 260 ARG ALA SER MET ASN GLY SER HIS GLU ASP GLY GLY LYS SEQRES 3 A 260 HIS ILE SER GLY GLY GLU ARG LEU ILE PRO PHE HIS GLU SEQRES 4 A 260 MET LYS HIS THR VAL ASN ALA LEU LEU GLU LYS GLY LEU SEQRES 5 A 260 SER HIS SER ARG GLY LYS PRO ASP PHE MET GLN ILE GLN SEQRES 6 A 260 PHE GLU GLU VAL HIS GLU SER ILE LYS THR ILE GLN PRO SEQRES 7 A 260 LEU PRO VAL HIS THR ASN GLU VAL SER CYS PRO GLU GLU SEQRES 8 A 260 GLY GLN LYS LEU ALA ARG LEU LEU LEU GLU LYS GLU GLY SEQRES 9 A 260 VAL SER ARG ASP VAL ILE GLU LYS ALA TYR GLU GLN ILE SEQRES 10 A 260 PRO GLU TRP SER ASP VAL ARG GLY ALA VAL LEU PHE ASP SEQRES 11 A 260 ILE HIS THR GLY LYS ARG MET ASP GLN THR LYS GLU LYS SEQRES 12 A 260 GLY VAL ARG VAL SER ARG MET ASP TRP PRO ASP ALA ASN SEQRES 13 A 260 PHE GLU LYS TRP ALA LEU HIS SER HIS VAL PRO ALA HIS SEQRES 14 A 260 SER ARG ILE LYS GLU ALA LEU ALA LEU ALA SER LYS VAL SEQRES 15 A 260 SER ARG HIS PRO ALA VAL VAL ALA GLU LEU CYS TRP SER SEQRES 16 A 260 ASP ASP PRO ASP TYR ILE THR GLY TYR VAL ALA GLY LYS SEQRES 17 A 260 LYS MET GLY TYR GLN ARG ILE THR ALA MET LYS GLU TYR SEQRES 18 A 260 GLY THR GLU GLU GLY CYS ARG VAL PHE PHE ILE ASP GLY SEQRES 19 A 260 SER ASN ASP VAL ASN THR TYR ILE HIS ASP LEU GLU LYS SEQRES 20 A 260 GLN PRO ILE LEU ILE GLU TRP GLU GLU ASP HIS ASP SER SEQRES 1 B 260 GLY ALA MET GLU GLU GLU THR PHE TYR SER VAL ARG MET SEQRES 2 B 260 ARG ALA SER MET ASN GLY SER HIS GLU ASP GLY GLY LYS SEQRES 3 B 260 HIS ILE SER GLY GLY GLU ARG LEU ILE PRO PHE HIS GLU SEQRES 4 B 260 MET LYS HIS THR VAL ASN ALA LEU LEU GLU LYS GLY LEU SEQRES 5 B 260 SER HIS SER ARG GLY LYS PRO ASP PHE MET GLN ILE GLN SEQRES 6 B 260 PHE GLU GLU VAL HIS GLU SER ILE LYS THR ILE GLN PRO SEQRES 7 B 260 LEU PRO VAL HIS THR ASN GLU VAL SER CYS PRO GLU GLU SEQRES 8 B 260 GLY GLN LYS LEU ALA ARG LEU LEU LEU GLU LYS GLU GLY SEQRES 9 B 260 VAL SER ARG ASP VAL ILE GLU LYS ALA TYR GLU GLN ILE SEQRES 10 B 260 PRO GLU TRP SER ASP VAL ARG GLY ALA VAL LEU PHE ASP SEQRES 11 B 260 ILE HIS THR GLY LYS ARG MET ASP GLN THR LYS GLU LYS SEQRES 12 B 260 GLY VAL ARG VAL SER ARG MET ASP TRP PRO ASP ALA ASN SEQRES 13 B 260 PHE GLU LYS TRP ALA LEU HIS SER HIS VAL PRO ALA HIS SEQRES 14 B 260 SER ARG ILE LYS GLU ALA LEU ALA LEU ALA SER LYS VAL SEQRES 15 B 260 SER ARG HIS PRO ALA VAL VAL ALA GLU LEU CYS TRP SER SEQRES 16 B 260 ASP ASP PRO ASP TYR ILE THR GLY TYR VAL ALA GLY LYS SEQRES 17 B 260 LYS MET GLY TYR GLN ARG ILE THR ALA MET LYS GLU TYR SEQRES 18 B 260 GLY THR GLU GLU GLY CYS ARG VAL PHE PHE ILE ASP GLY SEQRES 19 B 260 SER ASN ASP VAL ASN THR TYR ILE HIS ASP LEU GLU LYS SEQRES 20 B 260 GLN PRO ILE LEU ILE GLU TRP GLU GLU ASP HIS ASP SER HET PML A 301 11 HET 2PE A 302 7 HET COA B 301 31 HET PML B 302 11 HETNAM PML PIMELIC ACID HETNAM 2PE NONAETHYLENE GLYCOL HETNAM COA COENZYME A FORMUL 3 PML 2(C7 H12 O4) FORMUL 4 2PE C18 H38 O10 FORMUL 5 COA C21 H36 N7 O16 P3 S FORMUL 7 HOH *21(H2 O) HELIX 1 AA1 GLU A 38 SER A 52 1 15 HELIX 2 AA2 CYS A 87 GLY A 103 1 17 HELIX 3 AA3 SER A 105 ILE A 116 1 12 HELIX 4 AA4 PRO A 117 SER A 120 5 4 HELIX 5 AA5 PRO A 152 HIS A 164 1 13 HELIX 6 AA6 HIS A 168 HIS A 184 1 17 HELIX 7 AA7 ASP A 236 GLN A 247 1 12 HELIX 8 AA8 GLU B 38 SER B 52 1 15 HELIX 9 AA9 CYS B 87 GLY B 103 1 17 HELIX 10 AB1 SER B 105 ILE B 116 1 12 HELIX 11 AB2 PRO B 117 SER B 120 5 4 HELIX 12 AB3 PRO B 152 HIS B 164 1 13 HELIX 13 AB4 HIS B 168 ARG B 183 1 16 HELIX 14 AB5 ASP B 236 GLN B 247 1 12 SHEET 1 AA1 6 HIS A 26 PRO A 35 0 SHEET 2 AA1 6 PHE A 7 SER A 15 -1 N TYR A 8 O ILE A 34 SHEET 3 AA1 6 PHE A 60 GLU A 67 -1 O GLN A 64 N ARG A 11 SHEET 4 AA1 6 PHE B 60 GLU B 67 -1 O ILE B 63 N ILE A 63 SHEET 5 AA1 6 PHE B 7 SER B 15 -1 N ARG B 11 O GLN B 64 SHEET 6 AA1 6 HIS B 26 PRO B 35 -1 O ARG B 32 N VAL B 10 SHEET 1 AA2 3 LYS A 73 ILE A 75 0 SHEET 2 AA2 3 ILE A 249 ILE A 251 1 O LEU A 250 N LYS A 73 SHEET 3 AA2 3 MET A 149 ASP A 150 1 N ASP A 150 O ILE A 251 SHEET 1 AA3 6 VAL A 80 ASN A 83 0 SHEET 2 AA3 6 GLY A 210 ILE A 214 1 O ARG A 213 N ASN A 83 SHEET 3 AA3 6 GLY A 202 GLY A 206 -1 N VAL A 204 O GLN A 212 SHEET 4 AA3 6 VAL A 187 TRP A 193 -1 N CYS A 192 O TYR A 203 SHEET 5 AA3 6 CYS A 226 ILE A 231 -1 O CYS A 226 N TRP A 193 SHEET 6 AA3 6 VAL A 126 ASP A 129 1 N VAL A 126 O PHE A 229 SHEET 1 AA4 3 LYS B 73 ILE B 75 0 SHEET 2 AA4 3 ILE B 249 ILE B 251 1 O LEU B 250 N LYS B 73 SHEET 3 AA4 3 MET B 149 ASP B 150 1 N ASP B 150 O ILE B 251 SHEET 1 AA5 6 VAL B 80 ASN B 83 0 SHEET 2 AA5 6 GLY B 210 ILE B 214 1 O ARG B 213 N ASN B 83 SHEET 3 AA5 6 GLY B 202 GLY B 206 -1 N VAL B 204 O GLN B 212 SHEET 4 AA5 6 VAL B 187 TRP B 193 -1 N CYS B 192 O TYR B 203 SHEET 5 AA5 6 CYS B 226 ILE B 231 -1 O CYS B 226 N TRP B 193 SHEET 6 AA5 6 VAL B 126 ASP B 129 1 N VAL B 126 O PHE B 229 SITE 1 AC1 8 ARG A 170 ILE A 171 SER A 194 TYR A 199 SITE 2 AC1 8 THR A 201 TYR A 211 ARG A 213 2PE A 302 SITE 1 AC2 4 TRP A 119 VAL A 122 TRP A 193 PML A 301 SITE 1 AC3 6 GLU A 66 ARG B 13 PHE B 60 ARG B 123 SITE 2 AC3 6 LYS B 142 ARG B 145 SITE 1 AC4 8 ARG B 170 ILE B 171 TYR B 199 THR B 201 SITE 2 AC4 8 TYR B 203 TYR B 211 ARG B 213 HOH B2002 CRYST1 50.590 78.360 166.430 90.00 90.00 90.00 P 21 21 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 0.019767 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006009 0.00000 MTRIX1 1 0.295400 -0.952500 -0.074100 23.41630 1 MTRIX2 1 -0.948300 -0.301700 0.098400 -4.47660 1 MTRIX3 1 -0.116100 0.041200 -0.992400 350.80710 1