HEADER HYDROLASE 21-FEB-19 6QSQ TITLE X-RAY CRYSTAL STRUCTURE OF THE R336L VIBRIO ALKALINE PHOSPHATASE TITLE 2 VARIANT. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKALINE PHOSPHATASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO SPLENDIDUS; SOURCE 3 ORGANISM_TAXID: 29497; SOURCE 4 GENE: BCT36_11160; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ENZYME DYNAMICS DISORDERED LOOP HOMODIMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.G.HJORLEIFSSON,R.HELLAND,B.ASGEIRSSON REVDAT 3 24-JAN-24 6QSQ 1 REMARK REVDAT 2 10-FEB-21 6QSQ 1 JRNL LINK REVDAT 1 29-JAN-20 6QSQ 0 JRNL AUTH J.G.HJORLEIFSSON,R.HELLAND,M.MAGNUSDOTTIR,B.ASGEIRSSON JRNL TITL THE HIGH CATALYTIC RATE OF THE COLD-ACTIVE VIBRIO ALKALINE JRNL TITL 2 PHOSPHATASE REQUIRES A HYDROGEN BONDING NETWORK INVOLVING A JRNL TITL 3 LARGE INTERFACE LOOP. JRNL REF FEBS OPEN BIO 2020 JRNL REFN ESSN 2211-5463 JRNL PMID 33197282 JRNL DOI 10.1002/2211-5463.13041 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31771 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1610 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3809 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.52000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.90000 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): 0.177 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.159 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.120 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.398 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6QSQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1292100793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 0.5.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33403 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 48.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.52600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3E2D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR CONDITIONS 20%(W/V) PEG 3350 REMARK 280 AND 0.2 M POTASSIUM FORMATE. PROTEIN CONDITIONS: 20 MM TRIS, 1 REMARK 280 MM MGSO4, 5 MM MGCL2, 1.3 MM DESTHIOBIOTIN, 0.25 M NACL, 15 % (V/ REMARK 280 V) ETHYLENE GLYCOL, PH 8.0., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.96100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.96100 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 1.000000 0.000000 0.000000 49.04100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.29800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.04100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.29800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 41.96100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.04100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 59.29800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 41.96100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.04100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 59.29800 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -233.0 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 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 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 ALA A 504 REMARK 465 TRP A 505 REMARK 465 SER A 506 REMARK 465 HIS A 507 REMARK 465 PRO A 508 REMARK 465 GLN A 509 REMARK 465 PHE A 510 REMARK 465 GLU A 511 REMARK 465 LYS A 512 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 2 CG CD OE1 OE2 REMARK 470 LYS A 4 CG CD CE NZ REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 185 CG CD CE NZ REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 LYS A 236 CG CD CE NZ REMARK 470 GLU A 239 CG CD OE1 OE2 REMARK 470 GLU A 260 CG CD OE1 OE2 REMARK 470 LYS A 335 NZ REMARK 470 LYS A 377 CD CE NZ REMARK 470 ASP A 379 CG OD1 OD2 REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 LYS A 394 CG CD CE NZ REMARK 470 LYS A 406 CG CD CE NZ REMARK 470 LEU A 418 CG CD1 CD2 REMARK 470 GLN A 420 CG CD OE1 NE2 REMARK 470 LYS A 422 CE NZ REMARK 470 GLU A 427 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 HOH A 920 O HOH A 933 1.69 REMARK 500 O HOH A 782 O HOH A 920 1.82 REMARK 500 O HOH A 706 O HOH A 753 2.00 REMARK 500 O GLY A 48 O HOH A 701 2.12 REMARK 500 OG SER A 65 O2 SO4 A 605 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 793 O HOH A 793 4555 0.68 REMARK 500 O HOH A 817 O HOH A 817 4555 1.09 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 479 CD GLU A 479 OE1 0.067 REMARK 500 GLU A 492 CD GLU A 492 OE2 -0.067 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 240 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 GLU A 492 OE1 - CD - OE2 ANGL. DEV. = 8.2 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 THR A 112 -118.87 -103.38 REMARK 500 ALA A 123 16.84 -148.93 REMARK 500 SER A 149 -169.46 -168.91 REMARK 500 SER A 223 -122.37 -124.17 REMARK 500 HIS A 316 173.95 174.19 REMARK 500 PRO A 333 153.63 -49.12 REMARK 500 THR A 464 -142.26 -121.17 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 ZN A 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 SER A 65 OG 123.9 REMARK 620 3 ASP A 315 OD2 97.0 86.7 REMARK 620 4 HIS A 316 NE2 112.2 121.8 101.5 REMARK 620 5 SO4 A 605 O2 98.7 63.3 150.1 95.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD2 REMARK 620 2 THR A 118 OG1 93.4 REMARK 620 3 GLU A 268 OE2 99.8 89.3 REMARK 620 4 HOH A 729 O 93.6 91.1 166.5 REMARK 620 5 HOH A 773 O 173.4 90.8 85.2 81.2 REMARK 620 6 HOH A 847 O 89.0 175.8 93.7 85.3 86.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 273 OD1 REMARK 620 2 ASP A 273 OD2 57.2 REMARK 620 3 HIS A 277 NE2 95.8 90.3 REMARK 620 4 HIS A 465 NE2 97.2 153.0 101.6 REMARK 620 5 SO4 A 605 S 112.6 88.8 145.2 94.5 REMARK 620 6 SO4 A 605 O2 83.7 80.3 169.3 89.1 30.5 REMARK 620 7 SO4 A 605 O4 138.0 94.2 116.1 101.8 29.4 59.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DTB A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E2D RELATED DB: PDB DBREF1 6QSQ A 1 502 UNP A0A2N7KUA1_VIBSP DBREF2 6QSQ A A0A2N7KUA1 24 525 SEQADV 6QSQ VAL A 41 UNP A0A2N7KUA ILE 64 CONFLICT SEQADV 6QSQ SER A 79 UNP A0A2N7KUA GLY 102 CONFLICT SEQADV 6QSQ LEU A 336 UNP A0A2N7KUA ARG 359 ENGINEERED MUTATION SEQADV 6QSQ LEU A 503 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ ALA A 504 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ TRP A 505 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ SER A 506 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ HIS A 507 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ PRO A 508 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ GLN A 509 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ PHE A 510 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ GLU A 511 UNP A0A2N7KUA EXPRESSION TAG SEQADV 6QSQ LYS A 512 UNP A0A2N7KUA EXPRESSION TAG SEQRES 1 A 512 ALA GLU ILE LYS ASN VAL ILE LEU MET ILE GLY ASP GLY SEQRES 2 A 512 MET GLY PRO GLN GLN VAL GLY LEU LEU GLU THR TYR ALA SEQRES 3 A 512 ASN GLN ALA PRO ASN SER ILE TYR LYS GLY ASN LYS THR SEQRES 4 A 512 ALA VAL TYR GLN LEU ALA GLN GLU GLY VAL ILE GLY SER SEQRES 5 A 512 SER LEU THR HIS PRO GLU ASP ALA ILE VAL VAL ASP SER SEQRES 6 A 512 ALA CYS SER ALA THR MET LEU ALA THR GLY ILE TYR SER SEQRES 7 A 512 SER SER GLU VAL ILE GLY ILE ASP SER GLN GLY ASN HIS SEQRES 8 A 512 VAL GLU THR VAL LEU GLU LYS ALA LYS LYS ALA GLY LYS SEQRES 9 A 512 ALA THR GLY LEU VAL SER ASP THR ARG LEU THR HIS ALA SEQRES 10 A 512 THR PRO ALA SER PHE ALA ALA HIS GLN PRO HIS ARG SER SEQRES 11 A 512 LEU GLU ASN GLN ILE ALA SER ASP MET LEU ALA THR GLY SEQRES 12 A 512 ALA ASP VAL MET LEU SER GLY GLY LEU ARG HIS TRP ILE SEQRES 13 A 512 PRO LYS SER THR ASN ASP LYS GLY GLU THR TYR LYS GLN SEQRES 14 A 512 LEU GLU LYS LEU THR GLN GLY ASP VAL TYR LEU LYS SER SEQRES 15 A 512 LYS ARG LYS ASP ASP ARG ASN LEU LEU THR GLU ALA GLU SEQRES 16 A 512 LYS ASP GLY TYR GLN LEU ALA PHE ASN ARG ASN MET LEU SEQRES 17 A 512 ASP ASP ALA LYS GLY ASP LYS LEU LEU GLY LEU PHE ALA SEQRES 18 A 512 TYR SER GLY MET ASP ASP GLY ILE ALA TYR SER ASN LYS SEQRES 19 A 512 LYS LYS SER GLY GLU ARG THR GLN PRO SER LEU LYS GLU SEQRES 20 A 512 MET THR GLN LYS ALA LEU ASN ILE LEU SER LYS ASP GLU SEQRES 21 A 512 ASP GLY PHE PHE LEU MET VAL GLU GLY GLY GLN ILE ASP SEQRES 22 A 512 TRP ALA GLY HIS SER ASN ASP ALA GLY THR MET LEU HIS SEQRES 23 A 512 GLU LEU LEU LYS PHE ASP GLU ALA ILE GLN THR VAL TYR SEQRES 24 A 512 GLU TRP ALA LYS ASP ARG GLU ASP THR ILE VAL ILE VAL SEQRES 25 A 512 THR ALA ASP HIS GLU THR GLY SER PHE GLY PHE SER TYR SEQRES 26 A 512 SER SER ASN ASP LEU PRO LYS PRO GLN LYS LEU SER GLY SEQRES 27 A 512 GLU ALA PHE ALA ASP ARG ASP TYR ALA PRO ASN PHE ASN SEQRES 28 A 512 PHE GLY ALA PHE ASP ILE LEU ASP GLY LEU TYR ASN GLN SEQRES 29 A 512 LYS GLN SER TYR TYR GLY MET ILE SER GLU PHE GLN LYS SEQRES 30 A 512 LEU ASP LYS SER LEU GLN THR PRO GLU LYS LEU ALA GLU SEQRES 31 A 512 ILE VAL ASN LYS ASN SER GLU PHE PRO ILE THR ALA GLU SEQRES 32 A 512 GLN ALA LYS ASN VAL LEU ALA SER LYS PRO ASN PRO TYR SEQRES 33 A 512 ARG LEU ALA GLN HIS LYS TYR LEU SER ALA GLU GLU VAL SEQRES 34 A 512 PRO ALA ILE ASN ASP PHE ASP ALA PHE PHE PRO TYR ASN SEQRES 35 A 512 ASP ARG GLY ASN LEU LEU ALA ARG GLU GLN ALA THR GLY SEQRES 36 A 512 GLN ASN ILE VAL TRP GLY THR GLY THR HIS THR HIS THR SEQRES 37 A 512 PRO VAL ASN VAL PHE ALA TRP GLY PRO ALA GLU LYS ILE SEQRES 38 A 512 LEU PRO VAL SER LYS ILE MET HIS HIS SER GLU LEU GLY SEQRES 39 A 512 GLU TYR ILE LYS GLN GLN VAL ASN LEU ALA TRP SER HIS SEQRES 40 A 512 PRO GLN PHE GLU LYS HET DTB A 601 15 HET ZN A 602 1 HET ZN A 603 1 HET MG A 604 1 HET SO4 A 605 5 HETNAM DTB 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETSYN DTB D-DESTHIOBIOTIN FORMUL 2 DTB C10 H18 N2 O3 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 MG MG 2+ FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *236(H2 O) HELIX 1 AA1 GLY A 15 ALA A 29 1 15 HELIX 2 AA2 THR A 39 GLY A 48 1 10 HELIX 3 AA3 ASP A 64 GLY A 75 1 12 HELIX 4 AA4 THR A 94 ALA A 102 1 9 HELIX 5 AA5 HIS A 116 SER A 121 1 6 HELIX 6 AA6 LEU A 131 GLY A 143 1 13 HELIX 7 AA7 GLY A 151 TRP A 155 5 5 HELIX 8 AA8 PRO A 157 LYS A 163 5 7 HELIX 9 AA9 GLY A 164 THR A 174 1 11 HELIX 10 AB1 ASN A 189 ASP A 197 1 9 HELIX 11 AB2 ASN A 204 ALA A 211 1 8 HELIX 12 AB3 ASP A 227 SER A 237 1 11 HELIX 13 AB4 SER A 244 SER A 257 1 14 HELIX 14 AB5 GLN A 271 SER A 278 1 8 HELIX 15 AB6 ASP A 280 LYS A 303 1 24 HELIX 16 AB7 GLY A 338 ALA A 342 5 5 HELIX 17 AB8 PHE A 355 ASN A 363 1 9 HELIX 18 AB9 SER A 367 LEU A 378 1 12 HELIX 19 AC1 ASP A 379 GLN A 383 5 5 HELIX 20 AC2 THR A 384 SER A 396 1 13 HELIX 21 AC3 THR A 401 ALA A 410 1 10 HELIX 22 AC4 PHE A 435 PHE A 439 5 5 HELIX 23 AC5 ARG A 444 ASN A 457 1 14 HELIX 24 AC6 PRO A 477 LEU A 482 1 6 HELIX 25 AC7 PRO A 483 SER A 485 5 3 HELIX 26 AC8 HIS A 490 GLN A 500 1 11 SHEET 1 AA110 GLN A 200 ALA A 202 0 SHEET 2 AA110 LEU A 216 LEU A 219 1 O LEU A 217 N GLN A 200 SHEET 3 AA110 VAL A 146 GLY A 150 1 N MET A 147 O GLY A 218 SHEET 4 AA110 ALA A 105 ARG A 113 1 N LEU A 108 O VAL A 146 SHEET 5 AA110 PHE A 263 GLY A 269 1 O GLU A 268 N VAL A 109 SHEET 6 AA110 ASN A 5 GLY A 11 1 N ILE A 10 O GLY A 269 SHEET 7 AA110 THR A 308 ALA A 314 1 O ILE A 311 N MET A 9 SHEET 8 AA110 VAL A 470 TRP A 475 -1 O PHE A 473 N VAL A 312 SHEET 9 AA110 VAL A 49 LEU A 54 -1 N VAL A 49 O ALA A 474 SHEET 10 AA110 ILE A 487 HIS A 489 1 O MET A 488 N LEU A 54 SHEET 1 AA2 2 GLU A 317 THR A 318 0 SHEET 2 AA2 2 HIS A 465 THR A 466 -1 O THR A 466 N GLU A 317 SHEET 1 AA3 2 GLY A 322 PHE A 323 0 SHEET 2 AA3 2 ILE A 458 VAL A 459 -1 O VAL A 459 N GLY A 322 SHEET 1 AA4 2 SER A 411 PRO A 413 0 SHEET 2 AA4 2 GLU A 428 PRO A 430 -1 O VAL A 429 N LYS A 412 LINK OD1 ASP A 12 ZN ZN A 603 1555 1555 1.90 LINK OD2 ASP A 12 MG MG A 604 1555 1555 2.02 LINK OG SER A 65 ZN ZN A 603 1555 1555 2.00 LINK OG1 THR A 118 MG MG A 604 1555 1555 2.06 LINK OE2 GLU A 268 MG MG A 604 1555 1555 2.02 LINK OD1 ASP A 273 ZN ZN A 602 1555 1555 2.25 LINK OD2 ASP A 273 ZN ZN A 602 1555 1555 2.41 LINK NE2 HIS A 277 ZN ZN A 602 1555 1555 2.10 LINK OD2 ASP A 315 ZN ZN A 603 1555 1555 1.99 LINK NE2 HIS A 316 ZN ZN A 603 1555 1555 2.01 LINK NE2 HIS A 465 ZN ZN A 602 1555 1555 2.19 LINK ZN ZN A 602 S SO4 A 605 1555 1555 2.91 LINK ZN ZN A 602 O2 SO4 A 605 1555 1555 2.41 LINK ZN ZN A 602 O4 SO4 A 605 1555 1555 1.76 LINK ZN ZN A 603 O2 SO4 A 605 1555 1555 2.07 LINK MG MG A 604 O HOH A 729 1555 1555 2.22 LINK MG MG A 604 O HOH A 773 1555 1555 2.20 LINK MG MG A 604 O HOH A 847 1555 1555 2.16 SITE 1 AC1 2 TRP A 274 HOH A 833 SITE 1 AC2 4 ASP A 273 HIS A 277 HIS A 465 SO4 A 605 SITE 1 AC3 5 ASP A 12 SER A 65 ASP A 315 HIS A 316 SITE 2 AC3 5 SO4 A 605 SITE 1 AC4 6 ASP A 12 THR A 118 GLU A 268 HOH A 729 SITE 2 AC4 6 HOH A 773 HOH A 847 SITE 1 AC5 12 ASP A 12 SER A 65 ARG A 129 ASP A 273 SITE 2 AC5 12 HIS A 277 HIS A 316 HIS A 465 ZN A 602 SITE 3 AC5 12 ZN A 603 HOH A 703 HOH A 729 HOH A 738 CRYST1 98.082 118.596 83.922 90.00 90.00 90.00 C 2 2 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 0.010196 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008432 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011916 0.00000