HEADER HYDROLASE 07-OCT-16 5M16 TITLE STRUCTURE OF GH36 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN TITLE 2 COMPLEX WITH A HYDROLYSED CYCLOPROPYL CARBASUGAR. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-GALACTOSIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: GALA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-GALACTOSIDASE, GLYCOSIDE HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.PENGELLY,T.GLOSTER REVDAT 3 17-JAN-24 5M16 1 REMARK REVDAT 2 30-NOV-16 5M16 1 JRNL REVDAT 1 09-NOV-16 5M16 0 JRNL AUTH C.ADAMSON,R.J.PENGELLY,S.SHAMSI KAZEM ABADI,S.CHAKLADAR, JRNL AUTH 2 J.DRAPER,R.BRITTON,T.M.GLOSTER,A.J.BENNET JRNL TITL STRUCTURAL SNAPSHOTS FOR MECHANISM-BASED INACTIVATION OF A JRNL TITL 2 GLYCOSIDE HYDROLASE BY CYCLOPROPYL CARBASUGARS. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 55 14978 2016 JRNL REFN ESSN 1521-3773 JRNL PMID 27783466 JRNL DOI 10.1002/ANIE.201607431 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 78077 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 4059 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) : 1.62 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.66 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5763 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 276 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4316 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 355 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.26000 REMARK 3 B22 (A**2) : -1.45000 REMARK 3 B33 (A**2) : -1.81000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.081 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.069 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4570 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4247 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6222 ; 1.607 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9809 ; 0.847 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 556 ; 6.975 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;33.611 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 769 ;13.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;18.640 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 658 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5193 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1073 ; 0.002 ; 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): 2191 ; 2.333 ; 2.155 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2190 ; 2.331 ; 2.154 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2758 ; 3.016 ; 3.220 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2759 ; 3.016 ; 3.222 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2379 ; 3.668 ; 2.502 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2380 ; 3.668 ; 2.502 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3462 ; 5.195 ; 3.607 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5072 ; 5.989 ;25.222 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5073 ; 5.988 ;25.222 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 : 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 5M16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001670. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 82206 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 55.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.59400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5M0X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM SULFATE, 20% (W/V) PEG REMARK 280 3350 CRYSTALS WERE SOAKED FOR 7 DAYS IN 1 MM INHIBITOR, 30% (W/V) REMARK 280 PEG 3350 BEFORE FREEZING., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 34.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.02500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.01000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.02500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.01000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 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 -22 REMARK 465 GLY A -21 REMARK 465 SER A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLY A -10 REMARK 465 LEU A -9 REMARK 465 VAL A -8 REMARK 465 GLY A 526 REMARK 465 LYS A 527 REMARK 465 SER A 528 REMARK 465 SER A 529 REMARK 465 LEU A 530 REMARK 465 LYS A 531 REMARK 465 LYS A 532 REMARK 465 ARG A 533 REMARK 465 VAL A 534 REMARK 465 VAL A 535 REMARK 465 LYS A 536 REMARK 465 ARG A 537 REMARK 465 GLU A 538 REMARK 465 ASP A 539 REMARK 465 GLY A 540 REMARK 465 ARG A 541 REMARK 465 ASN A 542 REMARK 465 PHE A 543 REMARK 465 TYR A 544 REMARK 465 PHE A 545 REMARK 465 TYR A 546 REMARK 465 GLU A 547 REMARK 465 GLU A 548 REMARK 465 GLY A 549 REMARK 465 GLU A 550 REMARK 465 ARG A 551 REMARK 465 GLU A 552 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 LYS A 18 CD CE NZ REMARK 470 LYS A 28 CD CE NZ REMARK 470 LYS A 245 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A -6 CZ ARG A -6 NH2 0.106 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 -6 NE - CZ - NH1 ANGL. DEV. = -4.3 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 ARG A -6 -89.50 -76.00 REMARK 500 LEU A 31 2.94 81.62 REMARK 500 ASP A 82 109.07 -38.50 REMARK 500 TRP A 85 32.53 -142.50 REMARK 500 TYR A 104 -48.15 76.32 REMARK 500 ILE A 120 -56.06 -121.17 REMARK 500 ASP A 157 147.44 -171.47 REMARK 500 PHE A 194 -141.06 52.51 REMARK 500 ALA A 222 -37.81 156.93 REMARK 500 ASP A 229 66.50 -100.14 REMARK 500 PRO A 238 -160.64 -72.71 REMARK 500 PRO A 390 41.56 -78.09 REMARK 500 ASN A 399 35.22 -142.77 REMARK 500 ALA A 403 128.61 -174.15 REMARK 500 ARG A 420 -51.08 -128.67 REMARK 500 TRP A 422 -177.00 170.25 REMARK 500 ASP A 427 167.38 80.95 REMARK 500 ARG A 467 -149.36 -115.98 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 ARG A 383 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 419 OD2 REMARK 620 2 ASP A 454 OD2 87.3 REMARK 620 3 HOH A 723 O 86.1 94.7 REMARK 620 4 HOH A 909 O 92.5 87.7 177.2 REMARK 620 5 HOH A 953 O 177.7 90.5 93.4 88.1 REMARK 620 6 HOH A 955 O 91.7 173.7 91.5 86.1 90.5 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 SO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7D2 A 604 DBREF 5M16 A 1 552 UNP O33835 O33835_THEMT 1 552 SEQADV 5M16 MET A -22 UNP O33835 INITIATING METHIONINE SEQADV 5M16 GLY A -21 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A -20 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A -19 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -18 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -17 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -16 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -15 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -14 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -13 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A -12 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A -11 UNP O33835 EXPRESSION TAG SEQADV 5M16 GLY A -10 UNP O33835 EXPRESSION TAG SEQADV 5M16 LEU A -9 UNP O33835 EXPRESSION TAG SEQADV 5M16 VAL A -8 UNP O33835 EXPRESSION TAG SEQADV 5M16 PRO A -7 UNP O33835 EXPRESSION TAG SEQADV 5M16 ARG A -6 UNP O33835 EXPRESSION TAG SEQADV 5M16 GLY A -5 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A -4 UNP O33835 EXPRESSION TAG SEQADV 5M16 HIS A -3 UNP O33835 EXPRESSION TAG SEQADV 5M16 MET A -2 UNP O33835 EXPRESSION TAG SEQADV 5M16 ALA A -1 UNP O33835 EXPRESSION TAG SEQADV 5M16 SER A 0 UNP O33835 EXPRESSION TAG SEQRES 1 A 575 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 575 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET GLU ILE SEQRES 3 A 575 PHE GLY LYS THR PHE ARG GLU GLY ARG PHE VAL LEU LYS SEQRES 4 A 575 GLU LYS ASN PHE THR VAL GLU PHE ALA VAL GLU LYS ILE SEQRES 5 A 575 HIS LEU GLY TRP LYS ILE SER GLY ARG VAL LYS GLY SER SEQRES 6 A 575 PRO GLY ARG LEU GLU VAL LEU ARG THR LYS ALA PRO GLU SEQRES 7 A 575 LYS VAL LEU VAL ASN ASN TRP GLN SER TRP GLY PRO CYS SEQRES 8 A 575 ARG VAL VAL ASP ALA PHE SER PHE LYS PRO PRO GLU ILE SEQRES 9 A 575 ASP PRO ASN TRP ARG TYR THR ALA SER VAL VAL PRO ASP SEQRES 10 A 575 VAL LEU GLU ARG ASN LEU GLN SER ASP TYR PHE VAL ALA SEQRES 11 A 575 GLU GLU GLY LYS VAL TYR GLY PHE LEU SER SER LYS ILE SEQRES 12 A 575 ALA HIS PRO PHE PHE ALA VAL GLU ASP GLY GLU LEU VAL SEQRES 13 A 575 ALA TYR LEU GLU TYR PHE ASP VAL GLU PHE ASP ASP PHE SEQRES 14 A 575 VAL PRO LEU GLU PRO LEU VAL VAL LEU GLU ASP PRO ASN SEQRES 15 A 575 THR PRO LEU LEU LEU GLU LYS TYR ALA GLU LEU VAL GLY SEQRES 16 A 575 MET GLU ASN ASN ALA ARG VAL PRO LYS HIS THR PRO THR SEQRES 17 A 575 GLY TRP CYS SER TRP TYR HIS TYR PHE LEU ASP LEU THR SEQRES 18 A 575 TRP GLU GLU THR LEU LYS ASN LEU LYS LEU ALA LYS ASN SEQRES 19 A 575 PHE PRO PHE GLU VAL PHE GLN ILE ASP ASP ALA TYR GLU SEQRES 20 A 575 LYS ASP ILE GLY ASP TRP LEU VAL THR ARG GLY ASP PHE SEQRES 21 A 575 PRO SER VAL GLU GLU MET ALA LYS VAL ILE ALA GLU ASN SEQRES 22 A 575 GLY PHE ILE PRO GLY ILE TRP THR ALA PRO PHE SER VAL SEQRES 23 A 575 SER GLU THR SER ASP VAL PHE ASN GLU HIS PRO ASP TRP SEQRES 24 A 575 VAL VAL LYS GLU ASN GLY GLU PRO LYS MET ALA TYR ARG SEQRES 25 A 575 ASN TRP ASN LYS LYS ILE TYR ALA LEU ASP LEU SER LYS SEQRES 26 A 575 ASP GLU VAL LEU ASN TRP LEU PHE ASP LEU PHE SER SER SEQRES 27 A 575 LEU ARG LYS MET GLY TYR ARG TYR PHE LYS ILE ASP PHE SEQRES 28 A 575 LEU PHE ALA GLY ALA VAL PRO GLY GLU ARG LYS LYS ASN SEQRES 29 A 575 ILE THR PRO ILE GLN ALA PHE ARG LYS GLY ILE GLU THR SEQRES 30 A 575 ILE ARG LYS ALA VAL GLY GLU ASP SER PHE ILE LEU GLY SEQRES 31 A 575 CYS GLY SER PRO LEU LEU PRO ALA VAL GLY CYS VAL ASP SEQRES 32 A 575 GLY MET ARG ILE GLY PRO ASP THR ALA PRO PHE TRP GLY SEQRES 33 A 575 GLU HIS ILE GLU ASP ASN GLY ALA PRO ALA ALA ARG TRP SEQRES 34 A 575 ALA LEU ARG ASN ALA ILE THR ARG TYR PHE MET HIS ASP SEQRES 35 A 575 ARG PHE TRP LEU ASN ASP PRO ASP CYS LEU ILE LEU ARG SEQRES 36 A 575 GLU GLU LYS THR ASP LEU THR GLN LYS GLU LYS GLU LEU SEQRES 37 A 575 TYR SER TYR THR CYS GLY VAL LEU ASP ASN MET ILE ILE SEQRES 38 A 575 GLU SER ASP ASP LEU SER LEU VAL ARG ASP HIS GLY LYS SEQRES 39 A 575 LYS VAL LEU LYS GLU THR LEU GLU LEU LEU GLY GLY ARG SEQRES 40 A 575 PRO ARG VAL GLN ASN ILE MET SER GLU ASP LEU ARG TYR SEQRES 41 A 575 GLU ILE VAL SER SER GLY THR LEU SER GLY ASN VAL LYS SEQRES 42 A 575 ILE VAL VAL ASP LEU ASN SER ARG GLU TYR HIS LEU GLU SEQRES 43 A 575 LYS GLU GLY LYS SER SER LEU LYS LYS ARG VAL VAL LYS SEQRES 44 A 575 ARG GLU ASP GLY ARG ASN PHE TYR PHE TYR GLU GLU GLY SEQRES 45 A 575 GLU ARG GLU HET SO4 A 601 5 HET SO4 A 602 5 HET MG A 603 1 HET 7D2 A 604 13 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM 7D2 (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1- HETNAM 2 7D2 (HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3,4,5-TETROL FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 MG MG 2+ FORMUL 5 7D2 C8 H14 O5 FORMUL 6 HOH *355(H2 O) HELIX 1 AA1 GLY A -5 SER A 0 1 6 HELIX 2 AA2 TRP A 85 SER A 90 1 6 HELIX 3 AA3 VAL A 92 GLU A 97 1 6 HELIX 4 AA4 ASN A 159 ASN A 175 1 17 HELIX 5 AA5 SER A 189 PHE A 194 1 6 HELIX 6 AA6 LEU A 195 LEU A 197 5 3 HELIX 7 AA7 THR A 198 ALA A 209 1 12 HELIX 8 AA8 LYS A 210 PHE A 212 5 3 HELIX 9 AA9 SER A 239 ASN A 250 1 12 HELIX 10 AB1 SER A 267 HIS A 273 1 7 HELIX 11 AB2 PRO A 274 VAL A 277 5 4 HELIX 12 AB3 LYS A 302 GLY A 320 1 19 HELIX 13 AB4 PHE A 328 VAL A 334 5 7 HELIX 14 AB5 THR A 343 GLY A 360 1 18 HELIX 15 AB6 LEU A 372 VAL A 376 5 5 HELIX 16 AB7 ALA A 403 ARG A 414 1 12 HELIX 17 AB8 TYR A 415 HIS A 418 5 4 HELIX 18 AB9 THR A 439 LEU A 453 1 15 HELIX 19 AC1 ASP A 462 VAL A 466 5 5 HELIX 20 AC2 ARG A 467 GLU A 479 1 13 SHEET 1 AA1 6 LYS A 6 THR A 7 0 SHEET 2 AA1 6 GLU A 2 ILE A 3 -1 N ILE A 3 O LYS A 6 SHEET 3 AA1 6 ARG A 45 LYS A 52 -1 O ARG A 50 N GLU A 2 SHEET 4 AA1 6 GLU A 131 GLU A 137 -1 O ALA A 134 N VAL A 48 SHEET 5 AA1 6 HIS A 122 GLU A 128 -1 N PHE A 124 O TYR A 135 SHEET 6 AA1 6 LEU A 100 ASP A 103 -1 N SER A 102 O PHE A 125 SHEET 1 AA2 8 GLY A 11 LYS A 16 0 SHEET 2 AA2 8 PHE A 20 ILE A 29 -1 O VAL A 26 N GLY A 11 SHEET 3 AA2 8 GLY A 32 GLY A 41 -1 O ARG A 38 N GLU A 23 SHEET 4 AA2 8 LEU A 152 GLU A 156 -1 O LEU A 152 N ILE A 35 SHEET 5 AA2 8 LYS A 111 PHE A 115 -1 N GLY A 114 O VAL A 153 SHEET 6 AA2 8 PHE A 105 GLU A 108 -1 N VAL A 106 O TYR A 113 SHEET 7 AA2 8 LYS A 56 ASN A 60 -1 N LEU A 58 O ALA A 107 SHEET 8 AA2 8 CYS A 68 ASP A 72 -1 O ARG A 69 N VAL A 59 SHEET 1 AA3 4 GLY A 11 LYS A 16 0 SHEET 2 AA3 4 PHE A 20 ILE A 29 -1 O VAL A 26 N GLY A 11 SHEET 3 AA3 4 GLY A 32 GLY A 41 -1 O ARG A 38 N GLU A 23 SHEET 4 AA3 4 PHE A 143 PRO A 148 -1 O PHE A 143 N GLY A 41 SHEET 1 AA4 8 LEU A 423 ASP A 425 0 SHEET 2 AA4 8 GLY A 381 ARG A 383 1 N MET A 382 O ASP A 425 SHEET 3 AA4 8 PHE A 364 GLY A 367 1 N GLY A 367 O ARG A 383 SHEET 4 AA4 8 TYR A 323 ILE A 326 1 N PHE A 324 O LEU A 366 SHEET 5 AA4 8 ILE A 253 THR A 258 1 N THR A 258 O LYS A 325 SHEET 6 AA4 8 VAL A 216 ILE A 219 1 N PHE A 217 O ILE A 253 SHEET 7 AA4 8 THR A 185 CYS A 188 1 N TRP A 187 O GLN A 218 SHEET 8 AA4 8 ILE A 457 GLU A 459 1 O GLU A 459 N GLY A 186 SHEET 1 AA5 3 SER A 262 SER A 264 0 SHEET 2 AA5 3 LYS A 293 ALA A 297 -1 O TYR A 296 N VAL A 263 SHEET 3 AA5 3 MET A 286 ASN A 290 -1 N ALA A 287 O ILE A 295 SHEET 1 AA6 2 LYS A 279 GLU A 280 0 SHEET 2 AA6 2 GLU A 283 PRO A 284 -1 O GLU A 283 N GLU A 280 SHEET 1 AA7 4 ARG A 484 VAL A 487 0 SHEET 2 AA7 4 ARG A 496 THR A 504 -1 O VAL A 500 N ARG A 486 SHEET 3 AA7 4 GLY A 507 ASP A 514 -1 O ILE A 511 N ILE A 499 SHEET 4 AA7 4 GLU A 519 LYS A 524 -1 O GLU A 523 N LYS A 510 LINK OD2 ASP A 419 MG MG A 603 1555 1555 2.11 LINK OD2 ASP A 454 MG MG A 603 1555 1555 2.10 LINK MG MG A 603 O HOH A 723 1555 1555 2.04 LINK MG MG A 603 O HOH A 909 1555 1555 2.18 LINK MG MG A 603 O HOH A 953 1555 1555 2.10 LINK MG MG A 603 O HOH A 955 1555 1555 2.06 SITE 1 AC1 8 ARG A 9 GLY A 393 GLU A 394 HOH A 711 SITE 2 AC1 8 HOH A 793 HOH A 797 HOH A 867 HOH A 877 SITE 1 AC2 4 LYS A 302 ASP A 303 GLU A 304 LYS A 339 SITE 1 AC3 6 ASP A 419 ASP A 454 HOH A 723 HOH A 909 SITE 2 AC3 6 HOH A 953 HOH A 955 SITE 1 AC4 13 SER A -4 TRP A 65 TRP A 190 TYR A 191 SITE 2 AC4 13 ASP A 220 ASP A 221 TRP A 257 LYS A 325 SITE 3 AC4 13 ASP A 327 CYS A 368 ARG A 383 ASP A 387 SITE 4 AC4 13 HOH A 720 CRYST1 68.300 96.020 98.050 90.00 90.00 90.00 P 21 21 21 4 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 0.014641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010199 0.00000