HEADER LYASE 28-JUN-22 7YAX TITLE HYDROXYNITRILE LYASE FROM THE MILLIPEDE, COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYNITRILE LYASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OXIDUS GRACILIS; SOURCE 3 ORGANISM_TAXID: 291247; SOURCE 4 GENE: OGRAHNL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.CHAIKAEW,Y.WATANABE,D.ZHENG,F.MOTOJIMA,Y.ASANO REVDAT 2 19-JUN-24 7YAX 1 JRNL REVDAT 1 17-JAN-24 7YAX 0 JRNL AUTH S.CHAIKAEW,Y.WATANABE,D.ZHENG,F.MOTOJIMA,T.YAMAGUCHI,Y.ASANO JRNL TITL STRUCTURE-BASED SITE-DIRECTED MUTAGENESIS OF HYDROXYNITRILE JRNL TITL 2 LYASE FROM CYANOGENIC MILLIPEDE, OXIDUS GRACILIS FOR JRNL TITL 3 HYDROCYANATION AND HENRY REACTIONS. JRNL REF CHEMBIOCHEM V. 25 00118 2024 JRNL REFN ESSN 1439-7633 JRNL PMID 38526556 JRNL DOI 10.1002/CBIC.202400118 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.97 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 74268 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.882 REMARK 3 FREE R VALUE TEST SET COUNT : 3626 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 6.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 8.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1459 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5079 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 865 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.37400 REMARK 3 B22 (A**2) : 0.37400 REMARK 3 B33 (A**2) : -1.21300 REMARK 3 B12 (A**2) : 0.18700 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): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.063 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.225 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7YAX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300030563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 595005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 64.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22100 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: 6KFE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS (PH 5.5), 2.0 M REMARK 280 AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -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 64.56500 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 64.56500 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 64.56500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -258.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 B 492 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 505 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 517 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 518 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 522 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 LEU A 2 REMARK 465 TYR A 3 REMARK 465 TYR A 4 REMARK 465 VAL A 5 REMARK 465 SER A 6 REMARK 465 ILE A 7 REMARK 465 LEU A 8 REMARK 465 LEU A 9 REMARK 465 MET A 10 REMARK 465 ALA A 11 REMARK 465 VAL A 12 REMARK 465 TYR A 13 REMARK 465 ALA A 14 REMARK 465 VAL A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 ALA A 18 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 TYR B 3 REMARK 465 TYR B 4 REMARK 465 VAL B 5 REMARK 465 SER B 6 REMARK 465 ILE B 7 REMARK 465 LEU B 8 REMARK 465 LEU B 9 REMARK 465 MET B 10 REMARK 465 ALA B 11 REMARK 465 VAL B 12 REMARK 465 TYR B 13 REMARK 465 ALA B 14 REMARK 465 VAL B 15 REMARK 465 ALA B 16 REMARK 465 VAL B 17 REMARK 465 ALA B 18 REMARK 465 ASP B 19 REMARK 465 GLU B 20 REMARK 465 ASP B 21 REMARK 465 PRO B 22 REMARK 465 MET C 1 REMARK 465 LEU C 2 REMARK 465 TYR C 3 REMARK 465 TYR C 4 REMARK 465 VAL C 5 REMARK 465 SER C 6 REMARK 465 ILE C 7 REMARK 465 LEU C 8 REMARK 465 LEU C 9 REMARK 465 MET C 10 REMARK 465 ALA C 11 REMARK 465 VAL C 12 REMARK 465 TYR C 13 REMARK 465 ALA C 14 REMARK 465 VAL C 15 REMARK 465 ALA C 16 REMARK 465 VAL C 17 REMARK 465 ALA C 18 REMARK 465 ASP C 19 REMARK 465 GLU C 20 REMARK 465 ASP C 21 REMARK 465 MET D 1 REMARK 465 LEU D 2 REMARK 465 TYR D 3 REMARK 465 TYR D 4 REMARK 465 VAL D 5 REMARK 465 SER D 6 REMARK 465 ILE D 7 REMARK 465 LEU D 8 REMARK 465 LEU D 9 REMARK 465 MET D 10 REMARK 465 ALA D 11 REMARK 465 VAL D 12 REMARK 465 TYR D 13 REMARK 465 ALA D 14 REMARK 465 VAL D 15 REMARK 465 ALA D 16 REMARK 465 VAL D 17 REMARK 465 ALA D 18 REMARK 465 ASP D 19 REMARK 465 GLU D 20 REMARK 465 ASP D 21 REMARK 465 PRO D 22 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 OE1 GLN B 64 O HOH B 301 1.06 REMARK 500 HD21 ASN C 101 O HOH C 302 1.39 REMARK 500 HE22 GLN D 153 O HOH D 305 1.43 REMARK 500 HE22 GLN C 153 O HOH C 307 1.43 REMARK 500 HD1 HIS C 178 O HOH C 309 1.47 REMARK 500 ND2 ASN C 101 O HOH C 301 1.55 REMARK 500 HD1 HIS A 178 O HOH A 308 1.56 REMARK 500 HD21 ASN A 94 O HOH A 304 1.57 REMARK 500 HD1 HIS B 178 O HOH B 306 1.59 REMARK 500 O HOH C 433 O HOH C 478 1.73 REMARK 500 O HOH D 435 O HOH D 477 1.79 REMARK 500 O HOH C 418 O HOH C 501 1.84 REMARK 500 O HOH C 420 O HOH C 423 1.95 REMARK 500 O HOH C 302 O HOH C 312 1.97 REMARK 500 ND2 ASN C 101 O HOH C 302 1.99 REMARK 500 CD GLN B 64 O HOH B 301 2.01 REMARK 500 OD1 ASN A 94 O HOH A 301 2.07 REMARK 500 O HOH A 396 O HOH A 416 2.08 REMARK 500 O HOH C 384 O HOH C 437 2.11 REMARK 500 O HOH A 490 O HOH A 513 2.11 REMARK 500 O HOH D 368 O HOH D 418 2.12 REMARK 500 OE1 GLN C 64 O HOH C 303 2.12 REMARK 500 O HOH D 312 O HOH D 463 2.13 REMARK 500 N MET D 23 O HOH D 301 2.18 REMARK 500 O HOH D 359 O HOH D 463 2.18 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 C 478 O HOH D 460 2655 2.11 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 134 CD GLU A 134 OE1 0.095 REMARK 500 GLU B 37 CD GLU B 37 OE1 0.066 REMARK 500 GLU C 38 CD GLU C 38 OE2 -0.068 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 60 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG D 83 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG D 83 NE - CZ - NH2 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 LEU A 51 -61.93 -99.92 REMARK 500 ASN A 163 -4.47 74.04 REMARK 500 LEU B 51 -64.10 -98.48 REMARK 500 ASN B 163 -2.43 89.71 REMARK 500 LEU C 51 -64.78 -95.69 REMARK 500 ASN C 163 -3.61 86.80 REMARK 500 LEU D 51 -60.73 -95.05 REMARK 500 ASN D 116 70.12 -151.37 REMARK 500 ASN D 163 -4.78 85.29 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 B 60 0.10 SIDE CHAIN REMARK 500 ARG B 83 0.14 SIDE CHAIN REMARK 500 ARG C 60 0.11 SIDE CHAIN REMARK 500 ARG D 83 0.08 SIDE CHAIN 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 B 492 DISTANCE = 35.38 ANGSTROMS DBREF1 7YAX A 1 184 UNP A0A2Z5XCT7_9MYRI DBREF2 7YAX A A0A2Z5XCT7 1 184 DBREF1 7YAX B 1 184 UNP A0A2Z5XCT7_9MYRI DBREF2 7YAX B A0A2Z5XCT7 1 184 DBREF1 7YAX C 1 184 UNP A0A2Z5XCT7_9MYRI DBREF2 7YAX C A0A2Z5XCT7 1 184 DBREF1 7YAX D 1 184 UNP A0A2Z5XCT7_9MYRI DBREF2 7YAX D A0A2Z5XCT7 1 184 SEQRES 1 A 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 A 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 A 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 A 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 A 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 A 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 A 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 A 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 A 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 A 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 A 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 A 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 A 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 A 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 A 184 PHE TYR SEQRES 1 B 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 B 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 B 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 B 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 B 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 B 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 B 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 B 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 B 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 B 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 B 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 B 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 B 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 B 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 B 184 PHE TYR SEQRES 1 C 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 C 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 C 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 C 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 C 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 C 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 C 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 C 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 C 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 C 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 C 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 C 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 C 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 C 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 C 184 PHE TYR SEQRES 1 D 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 D 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 D 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 D 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 D 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 D 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 D 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 D 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 D 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 D 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 D 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 D 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 D 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 D 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 D 184 PHE TYR HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET CL A 204 1 HET SO4 B 201 5 HET SO4 B 202 5 HET SO4 B 203 5 HET CL B 204 1 HET SO4 C 201 5 HET SO4 C 202 5 HET SO4 C 203 5 HET CL C 204 1 HET SO4 D 201 5 HET SO4 D 202 5 HET SO4 D 203 5 HET CL D 204 1 HETNAM SO4 SULFATE ION HETNAM CL CHLORIDE ION FORMUL 5 SO4 12(O4 S 2-) FORMUL 8 CL 4(CL 1-) FORMUL 21 HOH *865(H2 O) HELIX 1 AA1 THR A 24 LEU A 28 5 5 HELIX 2 AA2 PRO A 35 ASN A 43 1 9 HELIX 3 AA3 THR A 52 ASP A 56 5 5 HELIX 4 AA4 ASP A 148 LYS A 160 1 13 HELIX 5 AA5 ASN A 163 ILE A 167 5 5 HELIX 6 AA6 THR B 24 LEU B 28 5 5 HELIX 7 AA7 PRO B 35 ASN B 43 1 9 HELIX 8 AA8 PRO B 93 ASN B 95 5 3 HELIX 9 AA9 ASP B 148 LYS B 160 1 13 HELIX 10 AB1 ASN B 163 ILE B 167 5 5 HELIX 11 AB2 THR C 24 LEU C 28 5 5 HELIX 12 AB3 PRO C 35 ASN C 43 1 9 HELIX 13 AB4 ASP C 148 LYS C 159 1 12 HELIX 14 AB5 ASN C 163 ILE C 167 5 5 HELIX 15 AB6 THR D 24 LEU D 28 5 5 HELIX 16 AB7 PRO D 35 LYS D 41 1 7 HELIX 17 AB8 THR D 52 ASP D 56 5 5 HELIX 18 AB9 ASP D 148 LYS D 160 1 13 HELIX 19 AC1 ASN D 163 ILE D 167 5 5 SHEET 1 AA110 HIS A 168 TYR A 169 0 SHEET 2 AA110 LEU A 45 VAL A 50 -1 N VAL A 50 O HIS A 168 SHEET 3 AA110 GLU A 134 ASN A 142 -1 O ASN A 142 N GLN A 46 SHEET 4 AA110 GLY A 122 ASN A 131 -1 N ASN A 131 O GLU A 134 SHEET 5 AA110 LYS A 107 THR A 119 -1 N ASN A 116 O SER A 124 SHEET 6 AA110 SER A 96 ASN A 101 -1 N ALA A 97 O TRP A 110 SHEET 7 AA110 ARG A 83 GLY A 92 -1 N VAL A 90 O ILE A 98 SHEET 8 AA110 ALA A 74 ARG A 80 -1 N ASP A 78 O ILE A 85 SHEET 9 AA110 THR A 59 VAL A 63 -1 N THR A 59 O ILE A 79 SHEET 10 AA110 LEU A 45 VAL A 50 -1 N LEU A 45 O ARG A 60 SHEET 1 AA210 HIS B 168 TYR B 169 0 SHEET 2 AA210 LEU B 45 VAL B 50 -1 N VAL B 50 O HIS B 168 SHEET 3 AA210 GLU B 134 ASN B 142 -1 O CYS B 140 N TYR B 49 SHEET 4 AA210 GLY B 122 ASN B 131 -1 N ASN B 131 O GLU B 134 SHEET 5 AA210 LYS B 107 THR B 119 -1 N ASN B 116 O SER B 124 SHEET 6 AA210 SER B 96 ASN B 101 -1 N ALA B 97 O TRP B 110 SHEET 7 AA210 ARG B 83 GLY B 92 -1 N VAL B 90 O ILE B 98 SHEET 8 AA210 ALA B 74 ARG B 80 -1 N ASP B 78 O ILE B 85 SHEET 9 AA210 THR B 59 VAL B 63 -1 N VAL B 63 O THR B 75 SHEET 10 AA210 LEU B 45 VAL B 50 -1 N LEU B 45 O ARG B 60 SHEET 1 AA310 HIS C 168 TYR C 169 0 SHEET 2 AA310 LEU C 45 VAL C 50 -1 N VAL C 50 O HIS C 168 SHEET 3 AA310 GLU C 134 ASN C 142 -1 O CYS C 140 N TYR C 49 SHEET 4 AA310 GLY C 122 ASN C 131 -1 N ASN C 131 O GLU C 134 SHEET 5 AA310 LYS C 107 THR C 119 -1 N ASN C 116 O SER C 124 SHEET 6 AA310 SER C 96 ASN C 101 -1 N ALA C 97 O TRP C 110 SHEET 7 AA310 ARG C 83 GLY C 92 -1 N VAL C 90 O ILE C 98 SHEET 8 AA310 ALA C 74 ARG C 80 -1 N ALA C 76 O ASN C 87 SHEET 9 AA310 THR C 59 VAL C 63 -1 N THR C 59 O ILE C 79 SHEET 10 AA310 LEU C 45 VAL C 50 -1 N LEU C 45 O ARG C 60 SHEET 1 AA410 HIS D 168 TYR D 169 0 SHEET 2 AA410 LEU D 45 VAL D 50 -1 N VAL D 50 O HIS D 168 SHEET 3 AA410 GLU D 134 ASN D 142 -1 O CYS D 140 N TYR D 49 SHEET 4 AA410 GLY D 122 ASN D 131 -1 N ASN D 131 O GLU D 134 SHEET 5 AA410 LYS D 107 THR D 119 -1 N ASN D 116 O SER D 124 SHEET 6 AA410 SER D 96 ASN D 101 -1 N ALA D 97 O TRP D 110 SHEET 7 AA410 ARG D 83 GLY D 92 -1 N VAL D 90 O ILE D 98 SHEET 8 AA410 ALA D 74 ARG D 80 -1 N ASP D 78 O ILE D 85 SHEET 9 AA410 THR D 59 VAL D 63 -1 N THR D 59 O ILE D 79 SHEET 10 AA410 LEU D 45 VAL D 50 -1 N LEU D 45 O ARG D 60 SSBOND 1 CYS A 25 CYS A 130 1555 1555 2.16 SSBOND 2 CYS A 57 CYS A 174 1555 1555 2.02 SSBOND 3 CYS A 102 CYS B 180 1555 1555 2.12 SSBOND 4 CYS A 126 CYS A 140 1555 1555 2.13 SSBOND 5 CYS A 180 CYS B 102 1555 1555 2.07 SSBOND 6 CYS B 25 CYS B 130 1555 1555 2.17 SSBOND 7 CYS B 57 CYS B 174 1555 1555 2.04 SSBOND 8 CYS B 126 CYS B 140 1555 1555 2.11 SSBOND 9 CYS C 25 CYS C 130 1555 1555 2.12 SSBOND 10 CYS C 57 CYS C 174 1555 1555 2.08 SSBOND 11 CYS C 102 CYS D 180 1555 1555 2.16 SSBOND 12 CYS C 126 CYS C 140 1555 1555 2.12 SSBOND 13 CYS C 180 CYS D 102 1555 1555 2.11 SSBOND 14 CYS D 25 CYS D 130 1555 1555 2.12 SSBOND 15 CYS D 57 CYS D 174 1555 1555 2.07 SSBOND 16 CYS D 126 CYS D 140 1555 1555 2.13 CISPEP 1 ASN A 43 PRO A 44 0 -15.13 CISPEP 2 ASN B 43 PRO B 44 0 -18.54 CISPEP 3 ASN C 43 PRO C 44 0 -17.44 CISPEP 4 ASN D 43 PRO D 44 0 -21.10 CRYST1 123.630 123.630 129.130 90.00 90.00 120.00 P 63 24 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 0.008089 0.004670 0.000000 0.00000 SCALE2 0.000000 0.009340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007744 0.00000