HEADER OXIDOREDUCTASE 03-MAR-17 5NCB TITLE CRYSTAL STRUCTURE OF AMYCOLATOPSIS CYTOCHROME P450 GCOA IN COMPLEX TITLE 2 WITH GUAIACOL. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME P450; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AMYCOLATOPSIS SP. ATCC 39116; SOURCE 3 ORGANISM_TAXID: 385957; SOURCE 4 GENE: WP_020419855; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYTOCHROME, P450, GUAIACOL, LIGNIN, CYP255A, AMYCOLATOPSIS, HEME, KEYWDS 2 HAEM, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.J.B.MALLINSON,C.W.JOHNSON,E.L.NEIDLE,G.T.BECKHAM,J.E.MCGEEHAN REVDAT 3 30-MAR-22 5NCB 1 REMARK REVDAT 2 11-JUL-18 5NCB 1 JRNL REVDAT 1 04-JUL-18 5NCB 0 JRNL AUTH S.J.B.MALLINSON,M.M.MACHOVINA,R.L.SILVEIRA,M.GARCIA-BORRAS, JRNL AUTH 2 N.GALLUP,C.W.JOHNSON,M.D.ALLEN,M.S.SKAF,M.F.CROWLEY, JRNL AUTH 3 E.L.NEIDLE,K.N.HOUK,G.T.BECKHAM,J.L.DUBOIS,J.E.MCGEEHAN JRNL TITL A PROMISCUOUS CYTOCHROME P450 AROMATIC O-DEMETHYLASE FOR JRNL TITL 2 LIGNIN BIOCONVERSION. JRNL REF NAT COMMUN V. 9 2487 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29950589 JRNL DOI 10.1038/S41467-018-04878-2 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 108389 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.151 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5812 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) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7894 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 461 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3164 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.41000 REMARK 3 B33 (A**2) : 0.81000 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): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.773 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.978 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3357 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2991 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4606 ; 1.710 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6918 ; 1.076 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 410 ; 5.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;32.377 ;23.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 472 ;11.180 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;21.399 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 487 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3824 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 719 ; 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): 1631 ; 1.579 ; 2.147 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1630 ; 1.568 ; 2.144 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2041 ; 2.008 ; 3.229 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2042 ; 2.009 ; 3.231 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1726 ; 2.702 ; 2.478 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1727 ; 2.701 ; 2.478 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2565 ; 3.202 ; 3.613 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3888 ; 3.240 ;26.488 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3826 ; 3.072 ;26.140 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6347 ; 2.743 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 202 ;20.827 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6348 ; 9.790 ; 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 5NCB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003728. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 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 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 114601 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 115.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 8.60 REMARK 200 R MERGE FOR SHELL (I) : 0.93100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, HEPES, GUAIACOL., REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 279K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -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 -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 57.87700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.04000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.04000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.81550 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.04000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.04000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.93850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.04000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.04000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.81550 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.04000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.04000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.93850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.87700 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: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 892 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MSE A 1 REMARK 465 THR A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 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 ASP A 213 OD1 OD2 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 ND2 ASN A 182 OE2 GLU A 184 0.85 REMARK 500 ND2 ASN A 182 CD GLU A 184 1.99 REMARK 500 CG ASN A 182 OE2 GLU A 184 2.13 REMARK 500 OD1 ASN A 182 O HOH A 601 2.14 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 ASN A 353 N ASN A 353 CA -0.123 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 118 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 118 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 280 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASN A 353 N - CA - C ANGL. DEV. = 16.3 DEGREES REMARK 500 ASN A 353 CA - C - O ANGL. DEV. = 15.8 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 ASN A 23 101.94 -164.38 REMARK 500 ALA A 35 80.53 -165.56 REMARK 500 TYR A 135 -60.16 -142.43 REMARK 500 LEU A 244 -89.99 -97.12 REMARK 500 SER A 294 54.33 -160.22 REMARK 500 LEU A 401 87.47 -150.87 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 902 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 903 DISTANCE = 8.01 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 HEM A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 356 SG REMARK 620 2 HEM A 501 NA 96.2 REMARK 620 3 HEM A 501 NB 88.6 88.7 REMARK 620 4 HEM A 501 NC 90.0 173.8 90.7 REMARK 620 5 HEM A 501 ND 97.0 91.1 174.4 88.9 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue JZ3 A 502 DBREF1 5NCB A 2 407 UNP A0A076MY51_AMYME DBREF2 5NCB A A0A076MY51 2 407 SEQADV 5NCB GLY A -1 UNP A0A076MY5 EXPRESSION TAG SEQADV 5NCB PRO A 0 UNP A0A076MY5 EXPRESSION TAG SEQADV 5NCB MSE A 1 UNP A0A076MY5 EXPRESSION TAG SEQADV 5NCB HIS A 210 UNP A0A076MY5 GLN 210 CONFLICT SEQRES 1 A 409 GLY PRO MSE THR THR THR GLU ARG PRO ASP LEU ALA TRP SEQRES 2 A 409 LEU ASP GLU VAL THR MSE THR GLN LEU GLU ARG ASN PRO SEQRES 3 A 409 TYR GLU VAL TYR GLU ARG LEU ARG ALA GLU ALA PRO LEU SEQRES 4 A 409 ALA PHE VAL PRO VAL LEU GLY SER TYR VAL ALA SER THR SEQRES 5 A 409 ALA GLU VAL CYS ARG GLU VAL ALA THR SER PRO ASP PHE SEQRES 6 A 409 GLU ALA VAL ILE THR PRO ALA GLY GLY ARG THR PHE GLY SEQRES 7 A 409 HIS PRO ALA ILE ILE GLY VAL ASN GLY ASP ILE HIS ALA SEQRES 8 A 409 ASP LEU ARG SER MSE VAL GLU PRO ALA LEU GLN PRO ALA SEQRES 9 A 409 GLU VAL ASP ARG TRP ILE ASP ASP LEU VAL ARG PRO ILE SEQRES 10 A 409 ALA ARG ARG TYR LEU GLU ARG PHE GLU ASN ASP GLY HIS SEQRES 11 A 409 ALA GLU LEU VAL ALA GLN TYR CYS GLU PRO VAL SER VAL SEQRES 12 A 409 ARG SER LEU GLY ASP LEU LEU GLY LEU GLN GLU VAL ASP SEQRES 13 A 409 SER ASP LYS LEU ARG GLU TRP PHE ALA LYS LEU ASN ARG SEQRES 14 A 409 SER PHE THR ASN ALA ALA VAL ASP GLU ASN GLY GLU PHE SEQRES 15 A 409 ALA ASN PRO GLU GLY PHE ALA GLU GLY ASP GLN ALA LYS SEQRES 16 A 409 ALA GLU ILE ARG ALA VAL VAL ASP PRO LEU ILE ASP LYS SEQRES 17 A 409 TRP ILE GLU HIS PRO ASP ASP SER ALA ILE SER HIS TRP SEQRES 18 A 409 LEU HIS ASP GLY MSE PRO PRO GLY GLN THR ARG ASP ARG SEQRES 19 A 409 GLU TYR ILE TYR PRO THR ILE TYR VAL TYR LEU LEU GLY SEQRES 20 A 409 ALA MSE GLN GLU PRO GLY HIS GLY MSE ALA SER THR LEU SEQRES 21 A 409 VAL GLY LEU PHE SER ARG PRO GLU GLN LEU GLU GLU VAL SEQRES 22 A 409 VAL ASP ASP PRO THR LEU ILE PRO ARG ALA ILE ALA GLU SEQRES 23 A 409 GLY LEU ARG TRP THR SER PRO ILE TRP SER ALA THR ALA SEQRES 24 A 409 ARG ILE SER THR LYS PRO VAL THR ILE ALA GLY VAL ASP SEQRES 25 A 409 LEU PRO ALA GLY THR PRO VAL MSE LEU SER TYR GLY SER SEQRES 26 A 409 ALA ASN HIS ASP THR GLY LYS TYR GLU ALA PRO SER GLN SEQRES 27 A 409 TYR ASP LEU HIS ARG PRO PRO LEU PRO HIS LEU ALA PHE SEQRES 28 A 409 GLY ALA GLY ASN HIS ALA CYS ALA GLY ILE TYR PHE ALA SEQRES 29 A 409 ASN HIS VAL MSE ARG ILE ALA LEU GLU GLU LEU PHE GLU SEQRES 30 A 409 ALA ILE PRO ASN LEU GLU ARG ASP THR ARG GLU GLY VAL SEQRES 31 A 409 GLU PHE TRP GLY TRP GLY PHE ARG GLY PRO THR SER LEU SEQRES 32 A 409 HIS VAL THR TRP GLU VAL MODRES 5NCB MSE A 17 MET MODIFIED RESIDUE MODRES 5NCB MSE A 94 MET MODIFIED RESIDUE MODRES 5NCB MSE A 224 MET MODIFIED RESIDUE MODRES 5NCB MSE A 247 MET MODIFIED RESIDUE MODRES 5NCB MSE A 254 MET MODIFIED RESIDUE MODRES 5NCB MSE A 318 MET MODIFIED RESIDUE MODRES 5NCB MSE A 366 MET MODIFIED RESIDUE HET MSE A 17 8 HET MSE A 94 8 HET MSE A 224 8 HET MSE A 247 8 HET MSE A 254 8 HET MSE A 318 8 HET MSE A 366 8 HET HEM A 501 43 HET JZ3 A 502 9 HETNAM MSE SELENOMETHIONINE HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM JZ3 GUAIACOL HETSYN HEM HEME HETSYN JZ3 2-METHOXYPHENOL FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 JZ3 C7 H8 O2 FORMUL 4 HOH *303(H2 O) HELIX 1 AA1 ARG A 6 VAL A 15 5 10 HELIX 2 AA2 THR A 16 ASN A 23 1 8 HELIX 3 AA3 PRO A 24 ALA A 35 1 12 HELIX 4 AA4 THR A 50 SER A 60 1 11 HELIX 5 AA5 THR A 68 GLY A 76 1 9 HELIX 6 AA6 ALA A 79 VAL A 83 5 5 HELIX 7 AA7 ASN A 84 GLU A 96 1 13 HELIX 8 AA8 PRO A 97 LEU A 99 5 3 HELIX 9 AA9 GLN A 100 ARG A 122 1 23 HELIX 10 AB1 LEU A 131 TYR A 135 1 5 HELIX 11 AB2 TYR A 135 GLY A 149 1 15 HELIX 12 AB3 ASP A 154 THR A 170 1 17 HELIX 13 AB4 ASN A 182 GLY A 185 5 4 HELIX 14 AB5 PHE A 186 HIS A 210 1 25 HELIX 15 AB6 SER A 214 ASP A 222 1 9 HELIX 16 AB7 ASP A 231 ARG A 264 1 34 HELIX 17 AB8 ARG A 264 ASP A 274 1 11 HELIX 18 AB9 LEU A 277 THR A 289 1 13 HELIX 19 AC1 SER A 320 ASN A 325 1 6 HELIX 20 AC2 GLY A 358 ILE A 377 1 20 SHEET 1 AA1 5 LEU A 37 VAL A 40 0 SHEET 2 AA1 5 SER A 45 ALA A 48 -1 O SER A 45 N VAL A 40 SHEET 3 AA1 5 PRO A 316 LEU A 319 1 O MSE A 318 N ALA A 48 SHEET 4 AA1 5 ALA A 297 SER A 300 -1 N ARG A 298 O VAL A 317 SHEET 5 AA1 5 PHE A 63 VAL A 66 -1 N GLU A 64 O ILE A 299 SHEET 1 AA2 3 HIS A 128 GLU A 130 0 SHEET 2 AA2 3 HIS A 402 THR A 404 -1 O VAL A 403 N ALA A 129 SHEET 3 AA2 3 GLU A 381 ARG A 382 -1 N GLU A 381 O THR A 404 SHEET 1 AA3 2 VAL A 304 ILE A 306 0 SHEET 2 AA3 2 VAL A 309 LEU A 311 -1 O LEU A 311 N VAL A 304 SHEET 1 AA4 2 PHE A 390 TRP A 391 0 SHEET 2 AA4 2 GLY A 397 PRO A 398 -1 O GLY A 397 N TRP A 391 LINK C THR A 16 N MSE A 17 1555 1555 1.32 LINK C MSE A 17 N THR A 18 1555 1555 1.33 LINK C SER A 93 N MSE A 94 1555 1555 1.33 LINK C MSE A 94 N VAL A 95 1555 1555 1.34 LINK C GLY A 223 N MSE A 224 1555 1555 1.34 LINK C MSE A 224 N PRO A 225 1555 1555 1.34 LINK C ALA A 246 N MSE A 247 1555 1555 1.35 LINK C MSE A 247 N GLN A 248 1555 1555 1.33 LINK C GLY A 253 N MSE A 254 1555 1555 1.33 LINK C MSE A 254 N ALA A 255 1555 1555 1.32 LINK C VAL A 317 N MSE A 318 1555 1555 1.33 LINK C MSE A 318 N LEU A 319 1555 1555 1.33 LINK C VAL A 365 N MSE A 366 1555 1555 1.34 LINK C MSE A 366 N ARG A 367 1555 1555 1.34 LINK SG CYS A 356 FE HEM A 501 1555 1555 2.41 CISPEP 1 HIS A 77 PRO A 78 0 -0.67 SITE 1 AC1 22 ILE A 80 ILE A 81 HIS A 88 ARG A 92 SITE 2 AC1 22 LEU A 99 TYR A 242 ALA A 246 GLU A 249 SITE 3 AC1 22 ILE A 292 THR A 296 ARG A 298 TYR A 321 SITE 4 AC1 22 ALA A 348 PHE A 349 GLY A 350 ALA A 351 SITE 5 AC1 22 HIS A 354 ALA A 355 CYS A 356 MSE A 366 SITE 6 AC1 22 JZ3 A 502 HOH A 689 SITE 1 AC2 7 VAL A 241 LEU A 244 GLY A 245 ALA A 246 SITE 2 AC2 7 ILE A 292 THR A 296 HEM A 501 CRYST1 104.080 104.080 115.754 90.00 90.00 90.00 P 43 21 2 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 0.009608 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008639 0.00000