HEADER HEME BINDING PROTEIN 26-MAY-15 5BNC TITLE STRUCTURE OF HEME BINDING PROTEIN MSMEG_6519 FROM MYCOBACTERIUM TITLE 2 SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEME BINDING PROTEIN MSMEG_6519; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRIDOXAMINE 5'-PHOSPHATE OXIDASE FAMILY PROTEIN, COMPND 5 PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED,FMN-BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: MSMEG_6519, MSMEI_6345, LJ00_32225; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HEME OXYGENASE, SPLIT BETA-BARREL, HEME BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.H.AHMED,P.D.CARR,C.J.JACKSON REVDAT 4 27-SEP-23 5BNC 1 LINK REVDAT 3 01-NOV-17 5BNC 1 JRNL REMARK REVDAT 2 11-NOV-15 5BNC 1 JRNL REVDAT 1 21-OCT-15 5BNC 0 JRNL AUTH F.H.AHMED,P.D.CARR,B.M.LEE,L.AFRIAT-JURNOU,A.E.MOHAMED, JRNL AUTH 2 N.S.HONG,J.FLANAGAN,M.C.TAYLOR,C.GREENING,C.J.JACKSON JRNL TITL SEQUENCE-STRUCTURE-FUNCTION CLASSIFICATION OF A JRNL TITL 2 CATALYTICALLY DIVERSE OXIDOREDUCTASE SUPERFAMILY IN JRNL TITL 3 MYCOBACTERIA. JRNL REF J.MOL.BIOL. V. 427 3554 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26434506 JRNL DOI 10.1016/J.JMB.2015.09.021 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29399 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1588 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2148 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2820 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3622 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : -0.34000 REMARK 3 B33 (A**2) : 1.09000 REMARK 3 B12 (A**2) : -0.17000 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): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.194 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.624 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3815 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3580 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5228 ; 1.766 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8206 ; 1.133 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 6.262 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;26.040 ;22.405 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 529 ;14.473 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;20.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 607 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4392 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 851 ; 0.005 ; 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): 1993 ; 2.474 ; 3.140 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1992 ; 2.469 ; 3.139 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2493 ; 3.736 ; 4.698 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 25 265 B 25 265 12398 0.130 0.050 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5BNC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000210197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31095 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 43.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.09700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.63700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2ARZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM ACETATE, 0.1M HEPES, REMARK 280 23% PEG3350, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 100.46867 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 200.93733 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 150.70300 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 251.17167 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 50.23433 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 300 REMARK: DIMER ACCORDING TO GEL FILTRATION 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: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 VAL B 15 REMARK 465 PRO B 16 REMARK 465 PRO B 17 REMARK 465 PRO B 18 REMARK 465 LEU B 19 REMARK 465 THR B 20 REMARK 465 PRO B 21 REMARK 465 VAL B 22 REMARK 465 ALA B 23 REMARK 465 ASP B 24 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 ARG A 163 CG CD NE CZ NH1 NH2 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 OG1 THR A 109 O2S EPE A 304 1.72 REMARK 500 O HOH A 432 O HOH A 492 2.09 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 107 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ARG B 107 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 107 NE - CZ - NH2 ANGL. DEV. = -3.8 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 ASP A 24 133.68 -36.72 REMARK 500 GLN A 265 27.05 -78.58 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 NI B 302 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 85 NE2 REMARK 620 2 HIS B 190 NE2 31.0 REMARK 620 3 HIS B 195 NE2 32.8 3.3 REMARK 620 4 HOH B 501 O 34.2 3.2 3.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 190 NE2 REMARK 620 2 HIS A 195 NE2 97.1 REMARK 620 3 HOH A 488 O 97.8 126.6 REMARK 620 4 HIS B 85 ND1 79.2 103.5 32.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 304 DBREF 5BNC A 15 266 UNP A0R6E4 A0R6E4_MYCS2 15 266 DBREF 5BNC B 15 266 UNP A0R6E4 A0R6E4_MYCS2 15 266 SEQRES 1 A 252 VAL PRO PRO PRO LEU THR PRO VAL ALA ASP VAL VAL ARG SEQRES 2 A 252 PRO SER ALA ALA GLU GLU ALA ARG THR ILE ALA ALA SER SEQRES 3 A 252 THR ASN VAL GLY THR LEU ALA THR LEU THR THR GLU GLY SEQRES 4 A 252 ASP PRO TRP ALA SER PHE VAL THR TYR GLY LEU LEU GLY SEQRES 5 A 252 GLY ALA PRO VAL LEU CYS VAL SER ASP MET ALA GLU HIS SEQRES 6 A 252 GLY ARG ASN LEU ALA HIS ASP PRO ARG ALA SER ILE ALA SEQRES 7 A 252 ILE VAL ALA PRO SER ALA GLU SER ASP PRO LEU ALA SER SEQRES 8 A 252 ALA ARG VAL THR LEU ALA GLY VAL ALA GLU ARG PRO GLU SEQRES 9 A 252 GLY ASP GLU LEU ALA ALA ALA ARG ALA ALA HIS LEU ASP SEQRES 10 A 252 ALA VAL ALA ALA ALA LYS TYR TYR ILE ASP TYR SER ASP SEQRES 11 A 252 PHE SER VAL TRP VAL LEU ARG VAL GLN ARG VAL ARG TRP SEQRES 12 A 252 VAL GLY GLY TYR GLY ARG MET ASP SER THR THR GLY GLU SEQRES 13 A 252 ALA TYR ALA ALA ALA GLU ALA ASP PRO VAL THR PRO ARG SEQRES 14 A 252 ALA ALA GLY ALA ILE ALA HIS LEU ASN ALA ASP HIS ALA SEQRES 15 A 252 ASP SER LEU LEU ALA MET ALA ARG ASN LEU GLY GLY TYR SEQRES 16 A 252 PRO ASP THR GLY GLU ALA VAL CYS THR GLY ALA ASP ARG SEQRES 17 A 252 TYR GLY LEU ASP LEU ARG VAL THR THR GLU ARG GLY VAL SEQRES 18 A 252 ALA TYR THR ARG VAL GLY TYR ALA ALA PRO ILE SER SER SEQRES 19 A 252 PHE ASP GLN LEU ARG ALA ALA THR VAL GLU LEU ALA GLN SEQRES 20 A 252 ARG ALA LYS GLN SER SEQRES 1 B 252 VAL PRO PRO PRO LEU THR PRO VAL ALA ASP VAL VAL ARG SEQRES 2 B 252 PRO SER ALA ALA GLU GLU ALA ARG THR ILE ALA ALA SER SEQRES 3 B 252 THR ASN VAL GLY THR LEU ALA THR LEU THR THR GLU GLY SEQRES 4 B 252 ASP PRO TRP ALA SER PHE VAL THR TYR GLY LEU LEU GLY SEQRES 5 B 252 GLY ALA PRO VAL LEU CYS VAL SER ASP MET ALA GLU HIS SEQRES 6 B 252 GLY ARG ASN LEU ALA HIS ASP PRO ARG ALA SER ILE ALA SEQRES 7 B 252 ILE VAL ALA PRO SER ALA GLU SER ASP PRO LEU ALA SER SEQRES 8 B 252 ALA ARG VAL THR LEU ALA GLY VAL ALA GLU ARG PRO GLU SEQRES 9 B 252 GLY ASP GLU LEU ALA ALA ALA ARG ALA ALA HIS LEU ASP SEQRES 10 B 252 ALA VAL ALA ALA ALA LYS TYR TYR ILE ASP TYR SER ASP SEQRES 11 B 252 PHE SER VAL TRP VAL LEU ARG VAL GLN ARG VAL ARG TRP SEQRES 12 B 252 VAL GLY GLY TYR GLY ARG MET ASP SER THR THR GLY GLU SEQRES 13 B 252 ALA TYR ALA ALA ALA GLU ALA ASP PRO VAL THR PRO ARG SEQRES 14 B 252 ALA ALA GLY ALA ILE ALA HIS LEU ASN ALA ASP HIS ALA SEQRES 15 B 252 ASP SER LEU LEU ALA MET ALA ARG ASN LEU GLY GLY TYR SEQRES 16 B 252 PRO ASP THR GLY GLU ALA VAL CYS THR GLY ALA ASP ARG SEQRES 17 B 252 TYR GLY LEU ASP LEU ARG VAL THR THR GLU ARG GLY VAL SEQRES 18 B 252 ALA TYR THR ARG VAL GLY TYR ALA ALA PRO ILE SER SER SEQRES 19 B 252 PHE ASP GLN LEU ARG ALA ALA THR VAL GLU LEU ALA GLN SEQRES 20 B 252 ARG ALA LYS GLN SER HET NI A 301 1 HET EPE A 302 15 HET EPE A 303 15 HET EPE A 304 15 HET EPE B 301 15 HET NI B 302 1 HET SO4 B 303 5 HET MG B 304 1 HETNAM NI NICKEL (II) ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETSYN EPE HEPES FORMUL 3 NI 2(NI 2+) FORMUL 4 EPE 4(C8 H18 N2 O4 S) FORMUL 9 SO4 O4 S 2- FORMUL 10 MG MG 2+ FORMUL 11 HOH *250(H2 O) HELIX 1 AA1 SER A 29 SER A 40 1 12 HELIX 2 AA2 ALA A 77 ASP A 86 1 10 HELIX 3 AA3 ASP A 101 ALA A 104 5 4 HELIX 4 AA4 GLU A 118 VAL A 133 1 16 HELIX 5 AA5 ALA A 134 TYR A 139 5 6 HELIX 6 AA6 GLY A 169 ALA A 175 1 7 HELIX 7 AA7 VAL A 180 ARG A 183 5 4 HELIX 8 AA8 ALA A 184 HIS A 195 1 12 HELIX 9 AA9 HIS A 195 LEU A 206 1 12 HELIX 10 AB1 SER A 248 ASP A 250 5 3 HELIX 11 AB2 GLN A 251 GLN A 265 1 15 HELIX 12 AB3 SER B 29 SER B 40 1 12 HELIX 13 AB4 ALA B 77 ASP B 86 1 10 HELIX 14 AB5 ASP B 101 ALA B 104 5 4 HELIX 15 AB6 GLU B 118 VAL B 133 1 16 HELIX 16 AB7 ALA B 134 TYR B 139 5 6 HELIX 17 AB8 GLY B 169 ALA B 175 1 7 HELIX 18 AB9 VAL B 180 PRO B 182 5 3 HELIX 19 AC1 ARG B 183 HIS B 195 1 13 HELIX 20 AC2 HIS B 195 LEU B 206 1 12 HELIX 21 AC3 ASP B 250 GLN B 265 1 16 SHEET 1 AA1 7 PRO A 55 THR A 61 0 SHEET 2 AA1 7 VAL A 43 LEU A 49 -1 N THR A 48 O TRP A 56 SHEET 3 AA1 7 ARG A 88 VAL A 94 -1 O SER A 90 N ALA A 47 SHEET 4 AA1 7 ALA A 106 GLU A 115 -1 O GLY A 112 N ALA A 89 SHEET 5 AA1 7 PHE A 145 GLY A 159 -1 O GLN A 153 N ALA A 111 SHEET 6 AA1 7 ALA A 68 SER A 74 -1 N VAL A 73 O SER A 146 SHEET 7 AA1 7 GLY A 63 LEU A 65 -1 N GLY A 63 O VAL A 70 SHEET 1 AA2 6 PRO A 55 THR A 61 0 SHEET 2 AA2 6 VAL A 43 LEU A 49 -1 N THR A 48 O TRP A 56 SHEET 3 AA2 6 ARG A 88 VAL A 94 -1 O SER A 90 N ALA A 47 SHEET 4 AA2 6 ALA A 106 GLU A 115 -1 O GLY A 112 N ALA A 89 SHEET 5 AA2 6 PHE A 145 GLY A 159 -1 O GLN A 153 N ALA A 111 SHEET 6 AA2 6 MET A 164 THR A 168 -1 O ASP A 165 N TRP A 157 SHEET 1 AA3 3 THR A 212 ALA A 220 0 SHEET 2 AA3 3 GLY A 224 THR A 231 -1 O THR A 230 N GLY A 213 SHEET 3 AA3 3 GLY A 234 GLY A 241 -1 O THR A 238 N LEU A 227 SHEET 1 AA4 7 PRO B 55 THR B 61 0 SHEET 2 AA4 7 VAL B 43 LEU B 49 -1 N LEU B 46 O SER B 58 SHEET 3 AA4 7 ARG B 88 VAL B 94 -1 O SER B 90 N ALA B 47 SHEET 4 AA4 7 ALA B 106 GLU B 115 -1 O GLY B 112 N ALA B 89 SHEET 5 AA4 7 PHE B 145 GLY B 159 -1 O GLN B 153 N ALA B 111 SHEET 6 AA4 7 ALA B 68 SER B 74 -1 N VAL B 73 O SER B 146 SHEET 7 AA4 7 GLY B 63 LEU B 65 -1 N GLY B 63 O VAL B 70 SHEET 1 AA5 6 PRO B 55 THR B 61 0 SHEET 2 AA5 6 VAL B 43 LEU B 49 -1 N LEU B 46 O SER B 58 SHEET 3 AA5 6 ARG B 88 VAL B 94 -1 O SER B 90 N ALA B 47 SHEET 4 AA5 6 ALA B 106 GLU B 115 -1 O GLY B 112 N ALA B 89 SHEET 5 AA5 6 PHE B 145 GLY B 159 -1 O GLN B 153 N ALA B 111 SHEET 6 AA5 6 MET B 164 THR B 168 -1 O ASP B 165 N TRP B 157 SHEET 1 AA6 3 ALA B 215 ALA B 220 0 SHEET 2 AA6 3 GLY B 224 THR B 231 -1 O ARG B 228 N VAL B 216 SHEET 3 AA6 3 GLY B 234 GLY B 241 -1 O VAL B 240 N LEU B 225 LINK NE2 HIS A 85 NI NI B 302 1555 5454 2.15 LINK NE2 HIS A 190 NI NI A 301 1555 1555 2.05 LINK NE2 HIS A 195 NI NI A 301 1555 1555 2.19 LINK NI NI A 301 O HOH A 488 1555 1555 2.30 LINK NI NI A 301 ND1 HIS B 85 5564 1555 2.05 LINK O SER B 143 MG MG B 304 1555 1555 2.58 LINK NE2 HIS B 190 NI NI B 302 1555 1555 1.99 LINK NE2 HIS B 195 NI NI B 302 1555 1555 2.13 LINK NI NI B 302 O HOH B 501 1555 1555 1.90 SITE 1 AC1 4 HIS A 190 HIS A 195 HOH A 488 HIS B 85 SITE 1 AC2 8 PHE A 59 VAL A 60 THR A 61 CYS A 72 SITE 2 AC2 8 HIS A 79 LEU B 103 ARG B 107 EPE B 301 SITE 1 AC3 9 LEU A 103 ARG A 107 ARG A 156 VAL A 158 SITE 2 AC3 9 MET A 164 EPE A 304 ALA B 77 GLU B 78 SITE 3 AC3 9 TYR B 139 SITE 1 AC4 8 ARG A 107 THR A 109 ARG A 156 EPE A 303 SITE 2 AC4 8 PHE B 59 THR B 61 HIS B 79 HOH B 469 SITE 1 AC5 7 ALA A 77 GLU A 78 EPE A 302 LEU B 103 SITE 2 AC5 7 ARG B 107 ARG B 156 HOH B 465 SITE 1 AC6 4 HIS A 85 HIS B 190 HIS B 195 HOH B 501 SITE 1 AC7 3 THR B 218 ASP B 226 HOH B 476 SITE 1 AC8 3 ASP B 75 SER B 143 SER B 146 CRYST1 62.100 62.100 301.406 90.00 90.00 120.00 P 61 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016103 0.009297 0.000000 0.00000 SCALE2 0.000000 0.018594 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003318 0.00000