PDB Short entry for 3PC4 HEADER LYASE 21-OCT-10 3PC4 TITLE FULL LENGTH STRUCTURE OF CYSTATHIONINE BETA-SYNTHASE FROM DROSOPHILA TITLE 2 IN COMPLEX WITH SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CG1753, ISOFORM A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CG1753, ISOFORM B, LD21426P; COMPND 5 EC: 4.2.1.22; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CG1753, DMEL_CG1753; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T1 KEYWDS CBS, SYNTHASE, PLP, HEME, CARBANION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KOUTMOS,J.L.SMITH REVDAT 4 06-SEP-23 3PC4 1 REMARK SEQADV LINK REVDAT 3 26-JUN-13 3PC4 1 REMARK VERSN REVDAT 2 05-JAN-11 3PC4 1 JRNL REVDAT 1 01-DEC-10 3PC4 0 JRNL AUTH M.KOUTMOS,O.KABIL,J.L.SMITH,R.BANERJEE JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE ACTIVATION AND REGULATION BY JRNL TITL 2 CYSTATHIONINE BETA-SYNTHASE (CBS) DOMAINS IN CYSTATHIONINE JRNL TITL 3 {BETA}-SYNTHASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 20958 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 21081698 JRNL DOI 10.1073/PNAS.1011448107 REMARK 2 REMARK 2 RESOLUTION. 1.70 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 52462 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2669 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3541 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.20 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3865 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 598 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : -0.24000 REMARK 3 B33 (A**2) : -0.57000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.069 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4016 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5462 ; 1.277 ; 2.013 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 5.879 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;34.560 ;24.845 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 699 ;13.350 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.483 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 608 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3005 ; 0.008 ; 0.021 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): 2515 ; 0.713 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4066 ; 1.306 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1501 ; 1.969 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1395 ; 3.279 ; 4.500 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 : BABINET MODEL WITH MASK 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: U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3PC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : K-B PAIR OF BIOMORPH MIRRORS FOR REMARK 200 VERTICAL AND HORIZONTAL FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3PC2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 0.2 LI2SO4, 100 MM BIS REMARK 280 -TRIS 6.5, VAPOR DIFFUSION, TEMPERATURE 298K, PH 6.5 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 37.56450 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 37.56450 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 46.47350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 68.96750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.47350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 68.96750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.56450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.47350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 68.96750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.56450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.47350 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 68.96750 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: 9190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38220 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -93.0 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 37.56450 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 -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 GLU A -1 REMARK 465 PHE A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 GLN A 3 REMARK 465 PRO A 4 REMARK 465 LYS A 5 REMARK 465 PRO A 6 REMARK 465 PRO A 511 REMARK 465 LYS A 512 REMARK 465 ALA A 513 REMARK 465 ASN A 514 REMARK 465 GLY A 515 REMARK 465 THR A 516 REMARK 465 THR A 517 REMARK 465 ASN A 518 REMARK 465 GLY A 519 REMARK 465 GLY A 520 REMARK 465 SER A 521 REMARK 465 HIS A 522 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 183 O HOH A 1034 2.13 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 807 O HOH A 1033 3555 2.10 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 GLU A 182 29.68 -67.57 REMARK 500 ASP A 190 80.79 70.44 REMARK 500 ASN A 197 -72.77 -69.35 REMARK 500 GLN A 268 -74.27 -113.49 REMARK 500 CYS A 300 -63.18 -92.77 REMARK 500 LYS A 353 -118.54 -115.25 REMARK 500 GLN A 509 -155.92 -123.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE UNBIASED ELECTRON DENSITY MAPS IN THE ABSENCE OF THE LIGAND KOU REMARK 600 SUGGEST THAT BEST MODELED LIGAND IS THAT OF A CARBANION WITH A REMARK 600 PLANAR C-ALPHA. BIOCHEMICAL DATA SUPPORTS THE ROLE OF LYSINE 88 IN REMARK 600 DEPROTONATION 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 701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 22 SG REMARK 620 2 HEM A 701 NA 92.8 REMARK 620 3 HEM A 701 NB 88.1 89.7 REMARK 620 4 HEM A 701 NC 85.3 178.1 89.7 REMARK 620 5 HEM A 701 ND 92.3 90.6 179.4 89.9 REMARK 620 6 HIS A 34 NE2 176.0 91.2 91.9 90.6 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 561 O REMARK 620 2 HOH A 589 O 73.8 REMARK 620 3 HOH A 867 O 123.7 74.3 REMARK 620 N 1 2 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 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KOU A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PC2 RELATED DB: PDB REMARK 900 RELATED ID: 3PC3 RELATED DB: PDB DBREF 3PC4 A 1 522 UNP Q9VRD9 Q9VRD9_DROME 1 522 SEQADV 3PC4 GLY A -4 UNP Q9VRD9 EXPRESSION TAG SEQADV 3PC4 SER A -3 UNP Q9VRD9 EXPRESSION TAG SEQADV 3PC4 PRO A -2 UNP Q9VRD9 EXPRESSION TAG SEQADV 3PC4 GLU A -1 UNP Q9VRD9 EXPRESSION TAG SEQADV 3PC4 PHE A 0 UNP Q9VRD9 EXPRESSION TAG SEQRES 1 A 527 GLY SER PRO GLU PHE MET PRO GLN PRO LYS PRO TYR GLU SEQRES 2 A 527 ARG PRO ALA ASP PHE ILE ASP PRO GLY LYS PRO SER LYS SEQRES 3 A 527 CYS LYS TRP HIS LEU GLY THR ALA GLU LYS SER PRO HIS SEQRES 4 A 527 ILE HIS ARG GLY ILE ALA HIS ARG GLN GLN ILE THR PRO SEQRES 5 A 527 ASN ILE LEU GLU VAL ILE GLY CYS THR PRO LEU VAL LYS SEQRES 6 A 527 LEU ASN ASN ILE PRO ALA SER ASP GLY ILE GLU CYS GLU SEQRES 7 A 527 MET TYR ALA LYS CYS GLU PHE LEU ASN PRO GLY GLY SER SEQRES 8 A 527 VAL LYS ASP ARG ILE GLY TYR ARG MET VAL GLN ASP ALA SEQRES 9 A 527 GLU GLU GLN GLY LEU LEU LYS PRO GLY TYR THR ILE ILE SEQRES 10 A 527 GLU PRO THR SER GLY ASN THR GLY ILE GLY LEU ALA MET SEQRES 11 A 527 ALA CYS ALA VAL LYS GLY TYR LYS CYS ILE ILE VAL MET SEQRES 12 A 527 PRO GLU LYS MET SER ASN GLU LYS VAL SER ALA LEU ARG SEQRES 13 A 527 THR LEU GLY ALA LYS ILE ILE ARG THR PRO THR GLU ALA SEQRES 14 A 527 ALA TYR ASP SER PRO GLU GLY LEU ILE TYR VAL ALA GLN SEQRES 15 A 527 GLN LEU GLN ARG GLU THR PRO ASN SER ILE VAL LEU ASP SEQRES 16 A 527 GLN TYR ARG ASN ALA GLY ASN PRO LEU ALA HIS TYR ASP SEQRES 17 A 527 GLY THR ALA ALA GLU ILE LEU TRP GLN LEU ASP ASN LYS SEQRES 18 A 527 VAL ASP MET ILE VAL VAL SER ALA GLY THR ALA GLY THR SEQRES 19 A 527 ILE SER GLY ILE GLY ARG LYS ILE LYS GLU GLN VAL PRO SEQRES 20 A 527 SER CYS GLN ILE VAL GLY VAL ASP PRO TYR GLY SER ILE SEQRES 21 A 527 LEU ALA ARG PRO ALA GLU LEU ASN LYS THR ASP VAL GLN SEQRES 22 A 527 PHE TYR GLU VAL GLU GLY ILE GLY TYR ASP PHE PRO PRO SEQRES 23 A 527 THR VAL PHE ASP ASP THR VAL VAL ASP VAL TRP THR LYS SEQRES 24 A 527 ILE GLY ASP SER ASP CYS PHE PRO MET SER ARG ARG LEU SEQRES 25 A 527 ASN ALA GLU GLU GLY LEU LEU CYS GLY GLY SER SER GLY SEQRES 26 A 527 GLY ALA MET HIS ALA ALA LEU GLU HIS ALA ARG LYS LEU SEQRES 27 A 527 LYS LYS GLY GLN ARG CYS VAL VAL ILE LEU PRO ASP GLY SEQRES 28 A 527 ILE ARG ASN TYR MET THR LYS PHE VAL SER ASP ASN TRP SEQRES 29 A 527 MET GLU ALA ARG ASN PHE LYS GLU PRO VAL ASN GLU HIS SEQRES 30 A 527 GLY HIS TRP TRP TRP SER LEU ALA ILE ALA GLU LEU GLU SEQRES 31 A 527 LEU PRO ALA PRO PRO VAL ILE LEU LYS SER ASP ALA THR SEQRES 32 A 527 VAL GLY GLU ALA ILE ALA LEU MET LYS LYS HIS ARG VAL SEQRES 33 A 527 ASP GLN LEU PRO VAL VAL ASP GLN ASP ASP GLY SER VAL SEQRES 34 A 527 LEU GLY VAL VAL GLY GLN GLU THR LEU ILE THR GLN ILE SEQRES 35 A 527 VAL SER MET ASN ARG GLN GLN SER ASP PRO ALA ILE LYS SEQRES 36 A 527 ALA LEU ASN LYS ARG VAL ILE ARG LEU ASN GLU SER GLU SEQRES 37 A 527 ILE LEU GLY LYS LEU ALA ARG VAL LEU GLU VAL ASP PRO SEQRES 38 A 527 SER VAL LEU ILE LEU GLY LYS ASN PRO ALA GLY LYS VAL SEQRES 39 A 527 GLU LEU LYS ALA LEU ALA THR LYS LEU ASP VAL THR THR SEQRES 40 A 527 PHE ILE ALA ALA GLY LYS GLN LYS PRO LYS ALA ASN GLY SEQRES 41 A 527 THR THR ASN GLY GLY SER HIS HET HEM A 701 43 HET KOU A 702 22 HET NA A 703 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM KOU (E)-N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY) HETNAM 2 KOU METHYL]PYRIDIN-4-YL}METHYLIDENE)-L-SERINE HETNAM NA SODIUM ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 KOU C11 H15 N2 O8 P FORMUL 4 NA NA 1+ FORMUL 5 HOH *598(H2 O) HELIX 1 1 ASN A 48 ILE A 53 5 6 HELIX 2 2 ASN A 63 ASP A 68 1 6 HELIX 3 3 PHE A 80 ASN A 82 5 3 HELIX 4 4 LYS A 88 GLN A 102 1 15 HELIX 5 5 GLY A 117 GLY A 131 1 15 HELIX 6 6 SER A 143 LEU A 153 1 11 HELIX 7 7 GLY A 171 GLU A 182 1 12 HELIX 8 8 ALA A 195 GLY A 204 1 10 HELIX 9 9 GLY A 204 LEU A 213 1 10 HELIX 10 10 ALA A 227 VAL A 241 1 15 HELIX 11 11 PRO A 259 LYS A 264 5 6 HELIX 12 12 ASP A 285 VAL A 289 5 5 HELIX 13 13 GLY A 296 GLY A 312 1 17 HELIX 14 14 GLY A 316 ARG A 331 1 16 HELIX 15 15 GLY A 346 MET A 351 5 6 HELIX 16 16 SER A 356 ARG A 363 1 8 HELIX 17 17 ALA A 380 GLU A 385 5 6 HELIX 18 18 THR A 398 ARG A 410 1 13 HELIX 19 19 GLN A 430 ASN A 441 1 12 HELIX 20 20 PRO A 447 LYS A 450 5 4 HELIX 21 21 ILE A 464 GLU A 473 1 10 HELIX 22 22 LYS A 497 ALA A 506 1 10 SHEET 1 A 6 LEU A 58 LYS A 60 0 SHEET 2 A 6 GLU A 73 CYS A 78 -1 O ALA A 76 N VAL A 59 SHEET 3 A 6 ARG A 338 LEU A 343 1 O VAL A 341 N LYS A 77 SHEET 4 A 6 MET A 219 SER A 223 1 N VAL A 221 O VAL A 340 SHEET 5 A 6 GLN A 245 PRO A 251 1 O VAL A 247 N ILE A 220 SHEET 6 A 6 VAL A 291 ILE A 295 1 O VAL A 291 N GLY A 248 SHEET 1 B 4 LYS A 156 THR A 160 0 SHEET 2 B 4 LYS A 133 PRO A 139 1 N ILE A 136 O LYS A 156 SHEET 3 B 4 THR A 110 PRO A 114 1 N ILE A 111 O ILE A 135 SHEET 4 B 4 SER A 186 ILE A 187 1 O ILE A 187 N ILE A 112 SHEET 1 C 4 LEU A 393 LYS A 394 0 SHEET 2 C 4 GLN A 413 VAL A 417 1 O PRO A 415 N LEU A 393 SHEET 3 C 4 VAL A 424 GLY A 429 -1 O LEU A 425 N VAL A 416 SHEET 4 C 4 LEU A 452 ASN A 453 -1 O ASN A 453 N VAL A 427 SHEET 1 D 3 ARG A 458 ASN A 460 0 SHEET 2 D 3 SER A 477 LYS A 483 1 O LEU A 481 N LEU A 459 SHEET 3 D 3 VAL A 489 THR A 496 -1 O GLU A 490 N GLY A 482 LINK SG CYS A 22 FE HEM A 701 1555 1555 2.40 LINK NE2 HIS A 34 FE HEM A 701 1555 1555 2.08 LINK O HOH A 561 NA NA A 703 1555 1555 2.29 LINK O HOH A 589 NA NA A 703 1555 1555 2.32 LINK NA NA A 703 O HOH A 867 1555 1555 2.30 CISPEP 1 ARG A 258 PRO A 259 0 -0.90 SITE 1 AC1 17 SER A 20 LYS A 21 CYS A 22 LYS A 23 SITE 2 AC1 17 TRP A 24 THR A 28 GLU A 30 PRO A 33 SITE 3 AC1 17 HIS A 34 ARG A 193 ALA A 195 PRO A 198 SITE 4 AC1 17 LEU A 199 TYR A 202 ARG A 235 THR A 282 SITE 5 AC1 17 HOH A 820 SITE 1 AC2 22 LYS A 88 THR A 115 SER A 116 ASN A 118 SITE 2 AC2 22 THR A 119 GLN A 191 ALA A 224 GLY A 225 SITE 3 AC2 22 THR A 226 ALA A 227 GLY A 228 THR A 229 SITE 4 AC2 22 GLY A 274 ILE A 275 TYR A 277 SER A 318 SITE 5 AC2 22 PRO A 344 ASP A 345 HOH A 623 HOH A 631 SITE 6 AC2 22 HOH A 667 HOH A 917 SITE 1 AC3 4 HIS A 324 HOH A 561 HOH A 589 HOH A 867 CRYST1 92.947 137.935 75.129 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 0.010759 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013310 0.00000