HEADER FLUORESCENT PROTEIN 17-APR-17 5VIK TITLE CRYSTAL STRUCTURE OF MONOMERIC NEAR-INFRARED FLUORESCENT PROTEIN TITLE 2 MIRFP703 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEAR-INFRARED FLUORESCENT PROTEIN MIRFP703; 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 4 23-OCT-24 5VIK 1 REMARK REVDAT 3 04-OCT-23 5VIK 1 REMARK REVDAT 2 04-OCT-17 5VIK 1 JRNL REMARK REVDAT 1 07-JUN-17 5VIK 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. 1.35 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 51889 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) : 0.123 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1666 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) : 1.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.44 REMARK 3 BIN R VALUE (WORKING SET) : 0.1860 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2299 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 280 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.39000 REMARK 3 B22 (A**2) : -1.63000 REMARK 3 B33 (A**2) : 0.29000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.03000 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): 0.055 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.979 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.983 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2555 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2484 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3494 ; 2.324 ; 2.000 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5709 ; 1.448 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 328 ; 7.026 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;29.794 ;22.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 431 ;13.517 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.884 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 385 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2954 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 599 ; 0.017 ; 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): 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): 5039 ; 7.343 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 78 ;23.238 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5172 ;12.354 ; 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 : 1.20 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 5VIK 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_1000227483. 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-BM 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 : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 29.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 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 (%): 31.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M NA CITRATE PH 5.0, 24% V/V REMARK 280 JEFFAMINE ED-2001 PH 7.0 0.4% N-OCTYL-BETA-D-GLUCOPYRANOSIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 26.41050 REMARK 290 SMTRY3 2 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 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 VAL A 2 REMARK 465 ALA A 3 REMARK 465 GLY A 4 REMARK 465 HIS A 5 REMARK 465 ALA A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 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 SER A 315 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 O HOH A 563 O HOH A 570 1.68 REMARK 500 O HOH A 548 O HOH A 714 1.86 REMARK 500 O HOH A 667 O HOH A 681 2.11 REMARK 500 O HOH A 744 O HOH A 747 2.17 REMARK 500 OG SER A 41 OD1 ASP A 44 2.19 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 548 O HOH A 726 2556 1.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 183 CG GLU A 183 CD -0.104 REMARK 500 GLU A 229 CD GLU A 229 OE1 -0.084 REMARK 500 GLU A 294 CD GLU A 294 OE2 -0.066 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 95 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 97 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 97 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 140 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 166 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 166 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 GLU A 183 OE1 - CD - OE2 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 196 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 196 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 ARG A 309 NE - CZ - NH1 ANGL. DEV. = 3.2 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 CYS A 20 8.11 85.26 REMARK 500 LEU A 27 50.89 -105.93 REMARK 500 ALA A 87 61.39 -159.05 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 781 DISTANCE = 6.40 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BLA A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VIQ RELATED DB: PDB REMARK 900 RELATED ID: 5VIV RELATED DB: PDB DBREF 5VIK A 1 315 PDB 5VIK 5VIK 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 LEU 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 ILE 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 BLA A 401 43 HETNAM BLA BILIVERDINE IX ALPHA FORMUL 2 BLA C33 H34 N4 O6 FORMUL 3 HOH *280(H2 O) HELIX 1 AA1 ASN A 53 ASN A 59 1 7 HELIX 2 AA2 PRO A 67 ASP A 72 1 6 HELIX 3 AA3 ASP A 72 LEU A 80 1 9 HELIX 4 AA4 PRO A 81 ASP A 84 5 4 HELIX 5 AA5 THR A 133 ALA A 144 1 12 HELIX 6 AA6 SER A 146 GLY A 163 1 18 HELIX 7 AA7 PRO A 198 VAL A 202 5 5 HELIX 8 AA8 PRO A 203 GLN A 213 1 11 HELIX 9 AA9 SER A 251 MET A 261 1 11 HELIX 10 AB1 ARG A 292 LEU A 313 1 22 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 VAL A 47 SER A 51 -1 N ALA A 50 O GLU A 229 SHEET 4 AA1 7 ALA A 36 VAL A 40 -1 N VAL A 39 O GLN A 49 SHEET 5 AA1 7 LEU A 117 ARG A 123 -1 O LEU A 121 N ALA A 36 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 VAL A 94 O GLY A 107 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 VAL A 269 O VAL A 281 SHEET 6 AA2 6 VAL A 215 LEU A 218 -1 N ARG A 216 O ALA A 268 LINK SG CYS A 20 CBC BLA A 401 1555 1555 1.78 CISPEP 1 ASN A 19 CYS A 20 0 6.30 CISPEP 2 MET A 90 PRO A 91 0 -0.35 CISPEP 3 ASN A 100 PRO A 101 0 -0.46 CISPEP 4 GLU A 229 PRO A 230 0 -18.61 SITE 1 AC1 23 CYS A 20 TYR A 170 TYR A 197 SER A 200 SITE 2 AC1 23 LEU A 201 VAL A 202 PRO A 203 TYR A 210 SITE 3 AC1 23 ARG A 216 ARG A 248 MET A 250 SER A 251 SITE 4 AC1 23 ILE A 253 HIS A 254 PHE A 257 ALA A 268 SITE 5 AC1 23 VAL A 282 HIS A 284 HOH A 552 HOH A 567 SITE 6 AC1 23 HOH A 575 HOH A 583 HOH A 673 CRYST1 36.319 52.821 64.622 90.00 92.53 90.00 P 1 21 1 2 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 0.027534 0.000000 0.001219 0.00000 SCALE2 0.000000 0.018932 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015490 0.00000