HEADER FLUORESCENT PROTEIN 17-APR-17 5VIV TITLE CRYSTAL STRUCTURE OF MONOMERIC NEAR-INFRARED FLUORESCENT PROTEIN TITLE 2 MIRFP670 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MONOMERIC NEAR-INFRARED FLUORESCENT PROTEIN MIRFP670; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOPSEUDOMONAS PALUSTRIS; SOURCE 3 ORGANISM_TAXID: 1076; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEAR-INFRARED FLUORESCENT PROTEIN, BILIVERDIN, PHYTOCHROME, RPBPHP1, KEYWDS 2 FLUORESCENT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.PLETNEV REVDAT 3 04-OCT-23 5VIV 1 COMPND HETNAM REVDAT 2 04-OCT-17 5VIV 1 JRNL REVDAT 1 21-JUN-17 5VIV 0 JRNL AUTH M.BALOBAN,D.M.SHCHERBAKOVA,S.PLETNEV,V.Z.PLETNEV, JRNL AUTH 2 J.C.LAGARIAS,V.V.VERKHUSHA JRNL TITL DESIGNING BRIGHTER NEAR-INFRARED FLUORESCENT PROTEINS: JRNL TITL 2 INSIGHTS FROM STRUCTURAL AND BIOCHEMICAL STUDIES. JRNL REF CHEM SCI V. 8 4546 2017 JRNL REFN ISSN 2041-6520 JRNL PMID 28936332 JRNL DOI 10.1039/C7SC00855D REMARK 2 REMARK 2 RESOLUTION. 1.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 67364 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2105 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) : 1.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2290 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2317 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.71 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.64000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : 2.23000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.034 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 4 REMARK 4 5VIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227499. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-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 : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.73500 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: 4XTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.4 M NACL, 0.08 M TRIS-HCL PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 26.26950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.69850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.64100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.69850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.26950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.64100 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 SER A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 PHE A 12 REMARK 465 GLY A 13 REMARK 465 THR A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 SER A 18 REMARK 465 ASN A 19 REMARK 465 GLU A 21 REMARK 465 HIS A 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 NH2 ARG A 212 O HOH A 1001 1.73 REMARK 500 O HOH A 1249 O HOH A 1257 1.89 REMARK 500 NH1 ARG A 212 O HOH A 1002 2.06 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 NH2 ARG A 196 O HOH A 1108 4445 2.14 REMARK 500 OG SER A 131 O HOH A 1111 3644 2.18 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 TYR A 164 CE1 TYR A 164 CZ -0.104 REMARK 500 SER A 182 CB SER A 182 OG -0.081 REMARK 500 TYR A 192 CE1 TYR A 192 CZ -0.079 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 97 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 253 CA - CB - SG ANGL. DEV. = -12.5 DEGREES REMARK 500 ARG A 296 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 301 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 301 NE - CZ - NH1 ANGL. DEV. = 10.0 DEGREES REMARK 500 ARG A 301 NE - CZ - NH2 ANGL. DEV. = -12.5 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 ALA A 3 -167.57 -126.13 REMARK 500 VAL A 63 -51.03 -135.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 9V1 IS BOUND FORM OF BILLEVERDIN IXA, LINKED TO THE PROTEIN WITH REMARK 600 TWO THIOESTER BONDS: ONE BETWEEN THE ATOM CBC OF 9V1 AND SG OF CYS REMARK 600 A20 AND ANOTHER BETWEEN THE ATOM CAC OF 9V1 AND SG OF CYS A253. 9UY REMARK 600 IS ALSO A BOUND FORM BILLEVERDIN IXA. 9UY HAS ONLY ONE THIOESTER REMARK 600 BOND WITH THE PROTEIN: BETWEEN THE ATOM CBC OF 9UY AND SG OF CYS REMARK 600 A253 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VIK RELATED DB: PDB REMARK 900 RELATED ID: 5VIQ RELATED DB: PDB DBREF 5VIV A 1 315 PDB 5VIV 5VIV 1 315 SEQRES 1 A 315 MET VAL ALA GLY HIS ALA SER GLY SER PRO ALA PHE GLY SEQRES 2 A 315 THR ALA SER HIS SER ASN CYS GLU HIS GLU GLU ILE HIS SEQRES 3 A 315 LEU ALA GLY SER ILE GLN PRO HIS GLY ALA LEU LEU VAL SEQRES 4 A 315 VAL SER GLU HIS ASP HIS ARG VAL ILE GLN ALA SER ALA SEQRES 5 A 315 ASN ALA ALA GLU PHE LEU ASN LEU GLY SER VAL LEU GLY SEQRES 6 A 315 VAL PRO LEU ALA GLU ILE ASP GLY ASP LEU LEU ILE LYS SEQRES 7 A 315 ILE LEU PRO HIS LEU ASP PRO THR ALA GLU GLY MET PRO SEQRES 8 A 315 VAL ALA VAL ARG CYS ARG ILE GLY ASN PRO SER THR GLU SEQRES 9 A 315 TYR CYS GLY LEU MET HIS ARG PRO PRO GLU GLY GLY LEU SEQRES 10 A 315 ILE ILE GLU LEU GLU ARG ALA GLY PRO SER ILE ASP LEU SEQRES 11 A 315 SER GLY THR LEU ALA PRO ALA LEU GLU ARG ILE ARG THR SEQRES 12 A 315 ALA GLY SER LEU ARG ALA LEU CYS ASP ASP THR VAL LEU SEQRES 13 A 315 LEU PHE GLN GLN CYS THR GLY TYR ASP ARG VAL MET VAL SEQRES 14 A 315 TYR ARG PHE ASP GLU GLN GLY HIS GLY LEU VAL PHE SER SEQRES 15 A 315 GLU CYS HIS VAL PRO GLY LEU GLU SER TYR PHE GLY ASN SEQRES 16 A 315 ARG TYR PRO SER SER THR VAL PRO GLN MET ALA ARG GLN SEQRES 17 A 315 LEU TYR VAL ARG GLN ARG VAL ARG VAL LEU VAL ASP VAL SEQRES 18 A 315 THR TYR GLN PRO VAL PRO LEU GLU PRO ARG LEU SER PRO SEQRES 19 A 315 LEU THR GLY ARG ASP LEU ASP MET SER GLY CYS PHE LEU SEQRES 20 A 315 ARG SER MET SER PRO CYS HIS LEU GLN PHE LEU LYS ASP SEQRES 21 A 315 MET GLY VAL ARG ALA THR LEU ALA VAL SER LEU VAL VAL SEQRES 22 A 315 GLY GLY LYS LEU TRP GLY LEU VAL VAL CYS HIS HIS TYR SEQRES 23 A 315 LEU PRO ARG PHE ILE ARG PHE GLU LEU ARG ALA ILE CYS SEQRES 24 A 315 LYS ARG LEU ALA GLU ARG ILE ALA THR ARG ILE THR ALA SEQRES 25 A 315 LEU GLU SER HET 9UY A 901 43 HET 9V1 A 902 43 HET CL A 903 1 HET CL A 904 1 HETNAM 9UY 3-[5-[[(3~{R},4~{R})-3-ETHENYL-4-METHYL-5- HETNAM 2 9UY OXIDANYLIDENE-3,4-DIHYDROPYRROL-2-YL]METHYL]-2-[[5- HETNAM 3 9UY [(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2-YL) HETNAM 4 9UY METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1~{H}- HETNAM 5 9UY PYRROL-2-YL]METHYL]-4-METHYL-1~{H}-PYRROL-3- HETNAM 6 9UY YL]PROPANOIC ACID HETNAM 9V1 3-[2-[[5-[(4-ETHENYL-3-METHYL-5-OXIDANYLIDENE-PYRROL-2- HETNAM 2 9V1 YL)METHYL]-3-(3-HYDROXY-3-OXOPROPYL)-4-METHYL-1~{H}- HETNAM 3 9V1 PYRROL-2-YL] METHYL]-5-[[(3~{R},4~{R})-3-ETHYL-4- HETNAM 4 9V1 METHYL-5-OXIDANYLIDENE-3,4-DIHYDROPYRROL-2-YL]METHYL]- HETNAM 5 9V1 4-METHYL-1~{H}-PYRROL-3-YL]PRO PANOIC ACID HETNAM CL CHLORIDE ION HETSYN 9UY BILLEVERDIN IXA, BOUND FORM HETSYN 9V1 BILLEVERDIN IXA, BOUND FORM FORMUL 2 9UY C33 H38 N4 O6 FORMUL 3 9V1 C33 H40 N4 O6 FORMUL 4 CL 2(CL 1-) FORMUL 6 HOH *314(H2 O) HELIX 1 AA1 GLU A 24 ALA A 28 5 5 HELIX 2 AA2 ASN A 53 ASN A 59 1 7 HELIX 3 AA3 PRO A 67 ILE A 71 5 5 HELIX 4 AA4 ASP A 74 LEU A 80 1 7 HELIX 5 AA5 PRO A 81 LEU A 83 5 3 HELIX 6 AA6 LEU A 130 THR A 143 1 14 HELIX 7 AA7 SER A 146 GLY A 163 1 18 HELIX 8 AA8 PRO A 198 VAL A 202 5 5 HELIX 9 AA9 PRO A 203 GLN A 213 1 11 HELIX 10 AB1 SER A 251 MET A 261 1 11 HELIX 11 AB2 ARG A 292 SER A 315 1 24 SHEET 1 AA1 7 SER A 30 ILE A 31 0 SHEET 2 AA1 7 VAL A 226 GLU A 229 -1 O VAL A 226 N ILE A 31 SHEET 3 AA1 7 ARG A 46 SER A 51 -1 N ALA A 50 O GLU A 229 SHEET 4 AA1 7 ALA A 36 SER A 41 -1 N VAL A 39 O GLN A 49 SHEET 5 AA1 7 LEU A 117 ARG A 123 -1 O ILE A 119 N LEU A 38 SHEET 6 AA1 7 THR A 103 HIS A 110 -1 N LEU A 108 O GLU A 120 SHEET 7 AA1 7 VAL A 92 ILE A 98 -1 N CYS A 96 O TYR A 105 SHEET 1 AA2 6 ARG A 196 TYR A 197 0 SHEET 2 AA2 6 GLY A 178 HIS A 185 -1 N GLY A 178 O TYR A 197 SHEET 3 AA2 6 ARG A 166 PHE A 172 -1 N ARG A 171 O LEU A 179 SHEET 4 AA2 6 LYS A 276 HIS A 285 -1 O LEU A 280 N TYR A 170 SHEET 5 AA2 6 ALA A 265 VAL A 273 -1 N LEU A 267 O CYS A 283 SHEET 6 AA2 6 VAL A 215 LEU A 218 -1 N LEU A 218 O THR A 266 LINK SG CYS A 20 CBC 9V1 A 902 1555 1555 1.63 LINK SG BCYS A 253 CBC 9UY A 901 1555 1555 1.65 LINK SG CCYS A 253 CAC 9V1 A 902 1555 1555 1.61 LINK O2D 9UY A 901 CGD 9V1 A 902 1555 1555 1.22 LINK CGD 9UY A 901 O2D 9V1 A 902 1555 1555 1.22 LINK CGD 9UY A 901 O1D 9V1 A 902 1555 1555 1.25 LINK CGD 9UY A 901 CBD 9V1 A 902 1555 1555 1.47 LINK O1D 9UY A 901 CGD 9V1 A 902 1555 1555 1.23 LINK CBD 9UY A 901 CAD 9V1 A 902 1555 1555 1.52 LINK CBD 9UY A 901 CGD 9V1 A 902 1555 1555 1.57 LINK CAD 9UY A 901 C3D 9V1 A 902 1555 1555 1.48 LINK CAD 9UY A 901 CBD 9V1 A 902 1555 1555 1.55 LINK C3D 9UY A 901 CAD 9V1 A 902 1555 1555 1.53 LINK C3D 9UY A 901 C2D 9V1 A 902 1555 1555 1.45 LINK C3D 9UY A 901 C4D 9V1 A 902 1555 1555 1.44 LINK C2D 9UY A 901 C3D 9V1 A 902 1555 1555 1.47 LINK C2D 9UY A 901 CMD 9V1 A 902 1555 1555 1.50 LINK C2D 9UY A 901 C1D 9V1 A 902 1555 1555 1.45 LINK CMD 9UY A 901 C2D 9V1 A 902 1555 1555 1.48 LINK C1D 9UY A 901 C2D 9V1 A 902 1555 1555 1.49 LINK C1D 9UY A 901 CHD 9V1 A 902 1555 1555 1.46 LINK C1D 9UY A 901 ND 9V1 A 902 1555 1555 1.35 LINK CHD 9UY A 901 C1D 9V1 A 902 1555 1555 1.51 LINK CHD 9UY A 901 C4C 9V1 A 902 1555 1555 1.32 LINK C4C 9UY A 901 CHD 9V1 A 902 1555 1555 1.38 LINK C4C 9UY A 901 C3C 9V1 A 902 1555 1555 1.47 LINK C4C 9UY A 901 NC 9V1 A 902 1555 1555 1.30 LINK C3C 9UY A 901 CAC 9V1 A 902 1555 1555 1.57 LINK C3C 9UY A 901 C2C 9V1 A 902 1555 1555 1.43 LINK C3C 9UY A 901 C4C 9V1 A 902 1555 1555 1.53 LINK CAC 9UY A 901 C3C 9V1 A 902 1555 1555 1.47 LINK CAC 9UY A 901 CBC 9V1 A 902 1555 1555 1.50 LINK CBC 9UY A 901 CAC 9V1 A 902 1555 1555 1.48 LINK C2C 9UY A 901 C3C 9V1 A 902 1555 1555 1.60 LINK C2C 9UY A 901 CMC 9V1 A 902 1555 1555 1.37 LINK C2C 9UY A 901 C1C 9V1 A 902 1555 1555 1.49 LINK C1C 9UY A 901 C2C 9V1 A 902 1555 1555 1.50 LINK C1C 9UY A 901 OC 9V1 A 902 1555 1555 1.13 LINK C1C 9UY A 901 NC 9V1 A 902 1555 1555 1.37 LINK OC 9UY A 901 C1C 9V1 A 902 1555 1555 1.27 LINK NC 9UY A 901 C1C 9V1 A 902 1555 1555 1.28 LINK NC 9UY A 901 C4C 9V1 A 902 1555 1555 1.34 LINK C4D 9UY A 901 CHA 9V1 A 902 1555 1555 1.47 LINK C4D 9UY A 901 C3D 9V1 A 902 1555 1555 1.48 LINK C4D 9UY A 901 ND 9V1 A 902 1555 1555 1.35 LINK ND 9UY A 901 C1D 9V1 A 902 1555 1555 1.35 LINK ND 9UY A 901 C4D 9V1 A 902 1555 1555 1.38 LINK CHA 9UY A 901 C1A 9V1 A 902 1555 1555 1.47 LINK CHA 9UY A 901 C4D 9V1 A 902 1555 1555 1.48 LINK C1A 9UY A 901 CHA 9V1 A 902 1555 1555 1.47 LINK C1A 9UY A 901 C2A 9V1 A 902 1555 1555 1.48 LINK C1A 9UY A 901 NA 9V1 A 902 1555 1555 1.32 LINK C2A 9UY A 901 C1A 9V1 A 902 1555 1555 1.45 LINK C2A 9UY A 901 CAA 9V1 A 902 1555 1555 1.52 LINK C2A 9UY A 901 C3A 9V1 A 902 1555 1555 1.43 LINK CAA 9UY A 901 C2A 9V1 A 902 1555 1555 1.48 LINK CAA 9UY A 901 CBA 9V1 A 902 1555 1555 1.50 LINK CBA 9UY A 901 CAA 9V1 A 902 1555 1555 1.54 LINK CBA 9UY A 901 CGA 9V1 A 902 1555 1555 1.49 LINK CGA 9UY A 901 CBA 9V1 A 902 1555 1555 1.50 LINK CGA 9UY A 901 O2A 9V1 A 902 1555 1555 1.21 LINK CGA 9UY A 901 O1A 9V1 A 902 1555 1555 1.20 LINK O2A 9UY A 901 CGA 9V1 A 902 1555 1555 1.27 LINK O1A 9UY A 901 CGA 9V1 A 902 1555 1555 1.18 LINK C3A 9UY A 901 C2A 9V1 A 902 1555 1555 1.45 LINK C3A 9UY A 901 CMA 9V1 A 902 1555 1555 1.50 LINK C3A 9UY A 901 C4A 9V1 A 902 1555 1555 1.44 LINK CMA 9UY A 901 C3A 9V1 A 902 1555 1555 1.48 LINK C4A 9UY A 901 C3A 9V1 A 902 1555 1555 1.49 LINK C4A 9UY A 901 NA 9V1 A 902 1555 1555 1.33 LINK C4A 9UY A 901 CHB 9V1 A 902 1555 1555 1.44 LINK NA 9UY A 901 C1A 9V1 A 902 1555 1555 1.36 LINK NA 9UY A 901 C4A 9V1 A 902 1555 1555 1.34 LINK CHB 9UY A 901 C4A 9V1 A 902 1555 1555 1.49 LINK CHB 9UY A 901 C1B 9V1 A 902 1555 1555 1.46 LINK C1B 9UY A 901 CHB 9V1 A 902 1555 1555 1.53 LINK C1B 9UY A 901 C2B 9V1 A 902 1555 1555 1.48 LINK C1B 9UY A 901 NB 9V1 A 902 1555 1555 1.29 LINK C2B 9UY A 901 C3B 9V1 A 902 1555 1555 1.41 LINK C2B 9UY A 901 CMB 9V1 A 902 1555 1555 1.52 LINK C2B 9UY A 901 C1B 9V1 A 902 1555 1555 1.48 LINK CMB 9UY A 901 C2B 9V1 A 902 1555 1555 1.48 LINK C3B 9UY A 901 CAB 9V1 A 902 1555 1555 1.41 LINK C3B 9UY A 901 C4B 9V1 A 902 1555 1555 1.48 LINK C3B 9UY A 901 C2B 9V1 A 902 1555 1555 1.51 LINK CAB 9UY A 901 C3B 9V1 A 902 1555 1555 1.57 LINK CAB 9UY A 901 CBB 9V1 A 902 1555 1555 1.28 LINK CBB 9UY A 901 CAB 9V1 A 902 1555 1555 1.37 LINK C4B 9UY A 901 C3B 9V1 A 902 1555 1555 1.47 LINK C4B 9UY A 901 OB 9V1 A 902 1555 1555 1.17 LINK C4B 9UY A 901 NB 9V1 A 902 1555 1555 1.40 LINK OB 9UY A 901 C4B 9V1 A 902 1555 1555 1.34 LINK NB 9UY A 901 C4B 9V1 A 902 1555 1555 1.30 LINK NB 9UY A 901 C1B 9V1 A 902 1555 1555 1.39 CISPEP 1 MET A 90 PRO A 91 0 1.10 CISPEP 2 ASN A 100 PRO A 101 0 8.78 CISPEP 3 GLU A 229 PRO A 230 0 -16.39 CRYST1 52.539 53.282 107.397 90.00 90.00 90.00 P 21 21 21 4 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 0.019033 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018768 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009311 0.00000