HEADER LYASE 09-JAN-17 5UGR TITLE MALYL-COA LYASE FROM METHYLOBACTERIUM EXTORQUENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALYL-COA LYASE/BETA-METHYLMALYL-COA LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.3.24; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHYLOBACTERIUM EXTORQUENS (STRAIN ATCC 14718 SOURCE 3 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1); SOURCE 4 ORGANISM_TAXID: 272630; SOURCE 5 STRAIN: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1; SOURCE 6 GENE: MCL, MEXAM1_META1P1733; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.GONZALEZ REVDAT 4 04-OCT-23 5UGR 1 REMARK REVDAT 3 23-AUG-17 5UGR 1 SPRSDE REMARK REVDAT 2 22-FEB-17 5UGR 1 JRNL REVDAT 1 08-FEB-17 5UGR 0 SPRSDE 23-AUG-17 5UGR 4ROQ JRNL AUTH J.M.GONZALEZ,R.MARTI-ARBONA,J.C.CHEN,C.J.UNKEFER JRNL TITL STRUCTURE OF METHYLOBACTERIUM EXTORQUENS MALYL-COA LYASE: JRNL TITL 2 COA-SUBSTRATE BINDING CORRELATES WITH DOMAIN SHIFT. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 73 79 2017 JRNL REF 2 BIOL COMMUN JRNL REFN ESSN 2053-230X JRNL PMID 28177317 JRNL DOI 10.1107/S2053230X17001029 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 59427 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) : 0.104 REMARK 3 R VALUE (WORKING SET) : 0.102 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3059 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3979 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.37 REMARK 3 BIN R VALUE (WORKING SET) : 0.1620 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.1880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2473 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 390 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.46000 REMARK 3 B22 (A**2) : 0.46000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : 0.23000 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): 0.051 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.049 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2629 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2570 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3559 ; 1.840 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5906 ; 1.220 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 6.139 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;33.323 ;23.644 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 463 ;14.045 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;21.016 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 399 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3002 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 0.004 ; 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): 1324 ; 2.340 ; 1.804 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1323 ; 2.232 ; 1.799 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1663 ; 2.664 ; 2.713 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1664 ; 2.704 ; 2.717 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1305 ; 3.726 ; 2.163 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1306 ; 3.725 ; 2.163 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1888 ; 4.110 ;89.412 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3299 ; 4.283 ;16.522 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3091 ; 3.809 ;15.521 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5195 ; 7.176 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 93 ;31.261 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5437 ;10.736 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5UGR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1000225846. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-14 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 : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.127092 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62486 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 38.440 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.1 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.52200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: 4L9Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 30 % W/V PEG 400, REMARK 280 0.2 M MGCL2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 34270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 68490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -267.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 63.26200 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 109.57300 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -63.26200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 109.57300 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 63.26200 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 109.57300 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 309.62100 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 309.62100 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 -63.26200 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 109.57300 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 309.62100 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 697 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 701 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 742 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 769 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 GLU A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 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 A 194 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 NH2 ARG A 212 O HOH A 501 1.30 REMARK 500 O HOH A 580 O HOH A 702 1.75 REMARK 500 O HOH A 767 O HOH A 825 1.77 REMARK 500 O PRO A 11 O HOH A 502 1.83 REMARK 500 O HOH A 805 O HOH A 835 1.98 REMARK 500 O HOH A 851 O HOH A 864 2.15 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 OE2 GLU A 283 O GLY A 323 4665 2.13 REMARK 500 O PRO A 11 O HOH A 855 4665 2.19 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 149 CD GLU A 149 OE1 0.087 REMARK 500 SER A 297 CB SER A 297 OG -0.089 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 87 CG - CD - NE ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG A 87 NE - CZ - NH1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 175 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 243 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 243 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 GLU A 251 OE1 - CD - OE2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 293 NE - CZ - NH1 ANGL. DEV. = 4.5 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 HIS A 14 48.97 -146.27 REMARK 500 GLU A 44 -115.30 -100.14 REMARK 500 GLU A 140 18.21 -142.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 885 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 886 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 887 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 888 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A 889 DISTANCE = 6.53 ANGSTROMS REMARK 525 HOH A 890 DISTANCE = 7.02 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 45 OD2 REMARK 620 2 GLU A 140 OE1 174.6 REMARK 620 3 ASP A 167 OD2 93.0 91.7 REMARK 620 4 HOH A 533 O 85.2 90.2 175.3 REMARK 620 5 HOH A 616 O 88.2 94.6 87.2 88.4 REMARK 620 6 HOH A 682 O 86.6 90.5 94.5 89.7 174.6 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1PE A 403 DBREF 5UGR A 1 324 UNP C5B113 C5B113_METEA 1 324 SEQADV 5UGR GLU A 325 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 326 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 327 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 328 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 329 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 330 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 331 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 332 UNP C5B113 EXPRESSION TAG SEQADV 5UGR HIS A 333 UNP C5B113 EXPRESSION TAG SEQRES 1 A 333 MET SER PHE THR LEU ILE GLN GLN ALA THR PRO ARG LEU SEQRES 2 A 333 HIS ARG SER GLU LEU ALA VAL PRO GLY SER ASN PRO THR SEQRES 3 A 333 PHE MET GLU LYS SER ALA ALA SER LYS ALA ASP VAL ILE SEQRES 4 A 333 PHE LEU ASP LEU GLU ASP ALA VAL ALA PRO ASP ASP LYS SEQRES 5 A 333 GLU GLN ALA ARG LYS ASN ILE ILE GLN ALA LEU ASN ASP SEQRES 6 A 333 LEU ASP TRP GLY ASN LYS THR MET MET ILE ARG ILE ASN SEQRES 7 A 333 GLY LEU ASP THR HIS TYR MET TYR ARG ASP VAL VAL ASP SEQRES 8 A 333 ILE VAL GLU ALA CYS PRO ARG LEU ASP MET ILE LEU ILE SEQRES 9 A 333 PRO LYS VAL GLY VAL PRO ALA ASP VAL TYR ALA ILE ASP SEQRES 10 A 333 VAL LEU THR THR GLN ILE GLU GLN ALA LYS LYS ARG GLU SEQRES 11 A 333 LYS LYS ILE GLY PHE GLU VAL LEU ILE GLU THR ALA LEU SEQRES 12 A 333 GLY MET ALA ASN VAL GLU ALA ILE ALA THR SER SER LYS SEQRES 13 A 333 ARG LEU GLU ALA MET SER PHE GLY VAL ALA ASP TYR ALA SEQRES 14 A 333 ALA SER THR ARG ALA ARG SER THR VAL ILE GLY GLY VAL SEQRES 15 A 333 ASN ALA ASP TYR SER VAL LEU THR ASP LYS ASP GLU ALA SEQRES 16 A 333 GLY ASN ARG GLN THR HIS TRP GLN ASP PRO TRP LEU PHE SEQRES 17 A 333 ALA GLN ASN ARG MET LEU VAL ALA CYS ARG ALA TYR GLY SEQRES 18 A 333 LEU ARG PRO ILE ASP GLY PRO PHE GLY ASP PHE SER ASP SEQRES 19 A 333 PRO ASP GLY TYR THR SER ALA ALA ARG ARG CYS ALA ALA SEQRES 20 A 333 LEU GLY PHE GLU GLY LYS TRP ALA ILE HIS PRO SER GLN SEQRES 21 A 333 ILE ASP LEU ALA ASN GLU VAL PHE THR PRO SER GLU ALA SEQRES 22 A 333 GLU VAL THR LYS ALA ARG ARG ILE LEU GLU ALA MET GLU SEQRES 23 A 333 GLU ALA ALA LYS ALA GLY ARG GLY ALA VAL SER LEU ASP SEQRES 24 A 333 GLY ARG LEU ILE ASP ILE ALA SER ILE ARG MET ALA GLU SEQRES 25 A 333 ALA LEU ILE GLN LYS ALA ASP ALA MET GLY GLY LYS GLU SEQRES 26 A 333 HIS HIS HIS HIS HIS HIS HIS HIS HET MG A 401 1 HET CL A 402 1 HET 1PE A 403 16 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 MG MG 2+ FORMUL 3 CL CL 1- FORMUL 4 1PE C10 H22 O6 FORMUL 5 HOH *390(H2 O) HELIX 1 AA1 ASN A 24 ALA A 33 1 10 HELIX 2 AA2 ALA A 48 ASP A 50 5 3 HELIX 3 AA3 ASP A 51 LEU A 66 1 16 HELIX 4 AA4 TYR A 84 CYS A 96 1 13 HELIX 5 AA5 VAL A 109 LYS A 128 1 20 HELIX 6 AA6 THR A 141 ASN A 147 1 7 HELIX 7 AA7 ASN A 147 ALA A 152 1 6 HELIX 8 AA8 GLY A 164 ARG A 173 1 10 HELIX 9 AA9 TRP A 206 GLY A 221 1 16 HELIX 10 AB1 ASP A 234 GLY A 249 1 16 HELIX 11 AB2 SER A 259 THR A 269 1 11 HELIX 12 AB3 SER A 271 GLY A 292 1 22 HELIX 13 AB4 ASP A 304 GLY A 323 1 20 SHEET 1 AA1 9 SER A 16 PRO A 21 0 SHEET 2 AA1 9 VAL A 38 ASP A 42 1 O ASP A 42 N VAL A 20 SHEET 3 AA1 9 THR A 72 ARG A 76 1 O MET A 74 N LEU A 41 SHEET 4 AA1 9 MET A 101 ILE A 104 1 O LEU A 103 N ILE A 75 SHEET 5 AA1 9 GLY A 134 ILE A 139 1 O GLU A 136 N ILE A 104 SHEET 6 AA1 9 LEU A 158 PHE A 163 1 O GLU A 159 N PHE A 135 SHEET 7 AA1 9 ARG A 223 ASP A 226 1 O ILE A 225 N MET A 161 SHEET 8 AA1 9 GLY A 252 ALA A 255 1 O GLY A 252 N ASP A 226 SHEET 9 AA1 9 SER A 16 PRO A 21 1 N GLU A 17 O ALA A 255 SHEET 1 AA2 2 SER A 187 LEU A 189 0 SHEET 2 AA2 2 THR A 200 TRP A 202 -1 O HIS A 201 N VAL A 188 SHEET 1 AA3 2 VAL A 296 LEU A 298 0 SHEET 2 AA3 2 ARG A 301 ILE A 303 -1 O ILE A 303 N VAL A 296 LINK OD2 ASP A 45 MG MG A 401 1555 1555 2.10 LINK OE1 GLU A 140 MG MG A 401 1555 1555 2.01 LINK OD2 ASP A 167 MG MG A 401 1555 1555 2.01 LINK MG MG A 401 O HOH A 533 1555 1555 2.06 LINK MG MG A 401 O HOH A 616 1555 1555 2.12 LINK MG MG A 401 O HOH A 682 1555 1555 2.07 SITE 1 AC1 6 ASP A 45 GLU A 140 ASP A 167 HOH A 533 SITE 2 AC1 6 HOH A 616 HOH A 682 SITE 1 AC2 5 GLY A 164 VAL A 165 ALA A 166 ASP A 167 SITE 2 AC2 5 HOH A 682 SITE 1 AC3 3 GLU A 94 ALA A 126 LYS A 127 CRYST1 126.524 126.524 103.207 90.00 90.00 120.00 P 6 2 2 12 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 0.007904 0.004563 0.000000 0.00000 SCALE2 0.000000 0.009126 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009689 0.00000