HEADER LYASE 29-SEP-16 5GZL TITLE CYCLODEAMINASE_PA COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE CYCLODEAMINASE; COMPND 3 CHAIN: B, A; COMPND 4 EC: 4.3.1.12; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES PRISTINAESPIRALIS; SOURCE 3 ORGANISM_TAXID: 38300; SOURCE 4 ATCC: 25846; SOURCE 5 GENE: PIPA, SPRI_0308, SPRI_7045; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS DIMER, COMPLEX, CYCLIZATION, DEAMINATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.YING,K.CHEN REVDAT 2 20-MAR-24 5GZL 1 REMARK REVDAT 1 17-JAN-18 5GZL 0 JRNL AUTH H.YING,K.CHEN JRNL TITL CYCLODEAMINASE_PA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 45046 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.137 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2403 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3271 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.16 REMARK 3 BIN R VALUE (WORKING SET) : 0.1240 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.1930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5256 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 526 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.147 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.684 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5494 ; 0.016 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5269 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7510 ; 1.741 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12081 ; 0.848 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 706 ; 6.519 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 229 ;36.863 ;22.664 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 828 ;13.335 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;22.089 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 871 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6239 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1212 ; 0.001 ; 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): 2830 ; 2.257 ; 2.019 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2829 ; 2.257 ; 2.019 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3534 ; 3.243 ; 3.009 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3535 ; 3.243 ; 3.009 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2664 ; 3.098 ; 2.352 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2664 ; 3.097 ; 2.351 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3977 ; 4.548 ; 3.396 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6364 ; 7.052 ;17.469 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6365 ; 7.051 ;17.470 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 : 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 REMARK 4 REMARK 4 5GZL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47575 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2%(V/V) POLYETHYLENE GLYCOL 400, 0.1M REMARK 280 HEPES, VAPOR DIFFUSION, SITTING 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 31.54700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.93750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.41250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.93750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.54700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.41250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -73.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 LEU B 348 REMARK 465 PRO B 349 REMARK 465 LEU B 350 REMARK 465 ALA B 351 REMARK 465 ALA B 352 REMARK 465 PRO B 353 REMARK 465 ALA B 354 REMARK 465 HIS B 355 REMARK 465 ALA A 354 REMARK 465 HIS A 355 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 HIS A 0 CG ND1 CD2 CE1 NE2 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 678 O HOH A 681 1.84 REMARK 500 O HOH A 699 O HOH A 718 1.97 REMARK 500 NH2 ARG A 274 O HOH A 501 2.02 REMARK 500 OE1 GLU B 191 O HOH B 501 2.04 REMARK 500 O LEU A 6 O HOH A 502 2.09 REMARK 500 OE1 GLU A 191 O HOH A 503 2.11 REMARK 500 OE1 GLU B 69 O HOH B 502 2.13 REMARK 500 O HOH B 546 O HOH B 703 2.13 REMARK 500 O HOH A 706 O HOH A 725 2.13 REMARK 500 O HOH A 722 O HOH A 752 2.15 REMARK 500 NH1 ARG A 43 OE1 GLU A 69 2.17 REMARK 500 O HOH B 712 O HOH A 666 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 B 735 O HOH A 666 4456 1.87 REMARK 500 O HOH B 697 O HOH B 740 4456 1.93 REMARK 500 CG1 VAL B 58 O HOH B 639 4456 1.99 REMARK 500 O HOH A 719 O HOH A 720 3656 2.10 REMARK 500 O HOH B 696 O HOH B 718 4556 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 GLU B 63 CD GLU B 63 OE2 -0.078 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 PRO B 57 C - N - CD ANGL. DEV. = 17.1 DEGREES REMARK 500 PRO B 217 C - N - CD ANGL. DEV. = 16.6 DEGREES REMARK 500 PRO A 57 C - N - CD ANGL. DEV. = 16.7 DEGREES REMARK 500 ARG A 181 NE - CZ - NH1 ANGL. DEV. = -4.8 DEGREES REMARK 500 PRO A 217 C - N - CD ANGL. DEV. = 16.9 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 B 72 -83.85 -109.99 REMARK 500 ASP B 72 -84.37 -109.66 REMARK 500 SER B 210 35.94 -93.18 REMARK 500 ALA B 235 123.97 -173.50 REMARK 500 ASP B 236 -84.59 -162.28 REMARK 500 ASP B 323 68.99 12.15 REMARK 500 MET A 1 151.97 -49.72 REMARK 500 ASP A 72 -77.77 -113.13 REMARK 500 ASP A 72 -78.15 -115.56 REMARK 500 SER A 210 36.89 -93.28 REMARK 500 ASP A 236 -85.18 -160.32 REMARK 500 ASP A 285 87.95 -152.00 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 756 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 757 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A 758 DISTANCE = 6.54 ANGSTROMS REMARK 525 HOH A 759 DISTANCE = 7.36 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GZI RELATED DB: PDB REMARK 900 RELATED ID: 5GZJ RELATED DB: PDB REMARK 900 RELATED ID: 5GZM RELATED DB: PDB DBREF 5GZL B 1 355 UNP D9UBW0 D9UBW0_STRPR 1 355 DBREF 5GZL A 1 355 UNP D9UBW0 D9UBW0_STRPR 1 355 SEQADV 5GZL ARG B -3 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL GLY B -2 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL SER B -1 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL HIS B 0 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL ARG A -3 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL GLY A -2 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL SER A -1 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZL HIS A 0 UNP D9UBW0 EXPRESSION TAG SEQRES 1 B 359 ARG GLY SER HIS MET GLU THR TRP VAL LEU GLY ARG ARG SEQRES 2 B 359 ASP VAL ALA GLU VAL VAL ALA ALA VAL GLY ARG ASP GLU SEQRES 3 B 359 LEU MET ARG ARG ILE ILE ASP ARG LEU THR GLY GLY LEU SEQRES 4 B 359 ALA GLU ILE GLY ARG GLY GLU ARG HIS LEU SER PRO LEU SEQRES 5 B 359 ARG GLY GLY LEU GLU ARG SER GLU PRO VAL PRO GLY ILE SEQRES 6 B 359 TRP GLU TRP MET PRO HIS ARG GLU PRO GLY ASP HIS ILE SEQRES 7 B 359 THR LEU LYS THR VAL GLY TYR SER PRO ALA ASN PRO ALA SEQRES 8 B 359 ARG PHE GLY LEU PRO THR ILE LEU GLY THR VAL ALA ARG SEQRES 9 B 359 TYR ASP ASP THR THR GLY ALA LEU THR ALA LEU MET ASP SEQRES 10 B 359 GLY VAL LEU LEU THR ALA LEU ARG THR GLY ALA ALA SER SEQRES 11 B 359 ALA VAL ALA SER ARG LEU LEU ALA ARG PRO ASP SER HIS SEQRES 12 B 359 THR LEU GLY LEU ILE GLY THR GLY ALA GLN ALA VAL THR SEQRES 13 B 359 GLN LEU HIS ALA LEU SER LEU VAL LEU PRO LEU GLN ARG SEQRES 14 B 359 ALA LEU VAL TRP ASP THR ASP PRO ALA HIS ARG GLU SER SEQRES 15 B 359 PHE ALA ARG ARG ALA ALA PHE THR GLY VAL SER VAL GLU SEQRES 16 B 359 ILE ALA GLU PRO ALA ARG ILE ALA ALA GLU ALA ASP VAL SEQRES 17 B 359 ILE SER THR ALA THR SER VAL ALA VAL GLY GLN GLY PRO SEQRES 18 B 359 VAL LEU PRO ASP THR GLY VAL ARG GLU HIS LEU HIS ILE SEQRES 19 B 359 ASN ALA VAL GLY ALA ASP LEU VAL GLY LYS THR GLU LEU SEQRES 20 B 359 PRO LEU GLY LEU LEU GLU ARG ALA PHE VAL THR ALA ASP SEQRES 21 B 359 HIS PRO GLU GLN ALA LEU ARG GLU GLY GLU CYS GLN GLN SEQRES 22 B 359 LEU SER ALA ASP ARG LEU GLY PRO GLN LEU ALA HIS LEU SEQRES 23 B 359 CYS ALA ASP PRO ALA ALA ALA ALA GLY ARG GLN ASP THR SEQRES 24 B 359 LEU SER VAL PHE ASP SER THR GLY PHE ALA PHE GLU ASP SEQRES 25 B 359 ALA LEU ALA MET GLU VAL PHE LEU GLU ALA ALA ALA GLU SEQRES 26 B 359 ARG ASP LEU GLY ILE ARG VAL GLY ILE GLU HIS HIS PRO SEQRES 27 B 359 GLY ASP ALA LEU ASP PRO TYR ALA LEU GLN PRO LEU PRO SEQRES 28 B 359 LEU PRO LEU ALA ALA PRO ALA HIS SEQRES 1 A 359 ARG GLY SER HIS MET GLU THR TRP VAL LEU GLY ARG ARG SEQRES 2 A 359 ASP VAL ALA GLU VAL VAL ALA ALA VAL GLY ARG ASP GLU SEQRES 3 A 359 LEU MET ARG ARG ILE ILE ASP ARG LEU THR GLY GLY LEU SEQRES 4 A 359 ALA GLU ILE GLY ARG GLY GLU ARG HIS LEU SER PRO LEU SEQRES 5 A 359 ARG GLY GLY LEU GLU ARG SER GLU PRO VAL PRO GLY ILE SEQRES 6 A 359 TRP GLU TRP MET PRO HIS ARG GLU PRO GLY ASP HIS ILE SEQRES 7 A 359 THR LEU LYS THR VAL GLY TYR SER PRO ALA ASN PRO ALA SEQRES 8 A 359 ARG PHE GLY LEU PRO THR ILE LEU GLY THR VAL ALA ARG SEQRES 9 A 359 TYR ASP ASP THR THR GLY ALA LEU THR ALA LEU MET ASP SEQRES 10 A 359 GLY VAL LEU LEU THR ALA LEU ARG THR GLY ALA ALA SER SEQRES 11 A 359 ALA VAL ALA SER ARG LEU LEU ALA ARG PRO ASP SER HIS SEQRES 12 A 359 THR LEU GLY LEU ILE GLY THR GLY ALA GLN ALA VAL THR SEQRES 13 A 359 GLN LEU HIS ALA LEU SER LEU VAL LEU PRO LEU GLN ARG SEQRES 14 A 359 ALA LEU VAL TRP ASP THR ASP PRO ALA HIS ARG GLU SER SEQRES 15 A 359 PHE ALA ARG ARG ALA ALA PHE THR GLY VAL SER VAL GLU SEQRES 16 A 359 ILE ALA GLU PRO ALA ARG ILE ALA ALA GLU ALA ASP VAL SEQRES 17 A 359 ILE SER THR ALA THR SER VAL ALA VAL GLY GLN GLY PRO SEQRES 18 A 359 VAL LEU PRO ASP THR GLY VAL ARG GLU HIS LEU HIS ILE SEQRES 19 A 359 ASN ALA VAL GLY ALA ASP LEU VAL GLY LYS THR GLU LEU SEQRES 20 A 359 PRO LEU GLY LEU LEU GLU ARG ALA PHE VAL THR ALA ASP SEQRES 21 A 359 HIS PRO GLU GLN ALA LEU ARG GLU GLY GLU CYS GLN GLN SEQRES 22 A 359 LEU SER ALA ASP ARG LEU GLY PRO GLN LEU ALA HIS LEU SEQRES 23 A 359 CYS ALA ASP PRO ALA ALA ALA ALA GLY ARG GLN ASP THR SEQRES 24 A 359 LEU SER VAL PHE ASP SER THR GLY PHE ALA PHE GLU ASP SEQRES 25 A 359 ALA LEU ALA MET GLU VAL PHE LEU GLU ALA ALA ALA GLU SEQRES 26 A 359 ARG ASP LEU GLY ILE ARG VAL GLY ILE GLU HIS HIS PRO SEQRES 27 A 359 GLY ASP ALA LEU ASP PRO TYR ALA LEU GLN PRO LEU PRO SEQRES 28 A 359 LEU PRO LEU ALA ALA PRO ALA HIS HET NAD B 401 44 HET LYS B 402 10 HET NAD A 401 44 HET LYS A 402 10 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM LYS LYSINE FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 LYS 2(C6 H15 N2 O2 1+) FORMUL 7 HOH *526(H2 O) HELIX 1 AA1 GLY B 7 GLY B 19 1 13 HELIX 2 AA2 GLY B 19 ARG B 40 1 22 HELIX 3 AA3 ALA B 84 GLY B 90 1 7 HELIX 4 AA4 GLY B 114 ALA B 134 1 21 HELIX 5 AA5 GLY B 147 LEU B 161 1 15 HELIX 6 AA6 ASP B 172 SER B 178 1 7 HELIX 7 AA7 SER B 178 ALA B 184 1 7 HELIX 8 AA8 PHE B 185 GLY B 187 5 3 HELIX 9 AA9 GLU B 194 ALA B 202 1 9 HELIX 10 AB1 PRO B 244 GLU B 249 1 6 HELIX 11 AB2 HIS B 257 GLY B 265 1 9 HELIX 12 AB3 GLU B 266 LEU B 270 5 5 HELIX 13 AB4 SER B 271 LEU B 275 5 5 HELIX 14 AB5 GLN B 278 ASP B 285 1 8 HELIX 15 AB6 PRO B 286 GLY B 291 1 6 HELIX 16 AB7 PHE B 304 ARG B 322 1 19 HELIX 17 AB8 GLY A 7 GLY A 19 1 13 HELIX 18 AB9 GLY A 19 ARG A 40 1 22 HELIX 19 AC1 ALA A 84 GLY A 90 1 7 HELIX 20 AC2 GLY A 114 ALA A 134 1 21 HELIX 21 AC3 GLY A 147 LEU A 159 1 13 HELIX 22 AC4 ASP A 172 SER A 178 1 7 HELIX 23 AC5 SER A 178 ALA A 184 1 7 HELIX 24 AC6 PHE A 185 GLY A 187 5 3 HELIX 25 AC7 GLU A 194 ALA A 202 1 9 HELIX 26 AC8 PRO A 244 GLU A 249 1 6 HELIX 27 AC9 HIS A 257 GLY A 265 1 9 HELIX 28 AD1 GLU A 266 LEU A 270 5 5 HELIX 29 AD2 SER A 271 LEU A 275 5 5 HELIX 30 AD3 GLN A 278 ASP A 285 1 8 HELIX 31 AD4 PRO A 286 ALA A 290 5 5 HELIX 32 AD5 PHE A 304 ARG A 322 1 19 SHEET 1 AA1 7 GLY B 50 ARG B 54 0 SHEET 2 AA1 7 GLY B 60 GLU B 69 -1 O GLY B 60 N ARG B 54 SHEET 3 AA1 7 HIS B 73 TYR B 81 -1 O HIS B 73 N GLU B 69 SHEET 4 AA1 7 ILE B 94 ASP B 102 -1 O LEU B 95 N GLY B 80 SHEET 5 AA1 7 LEU B 108 ASP B 113 -1 O ALA B 110 N ARG B 100 SHEET 6 AA1 7 THR B 3 LEU B 6 1 N LEU B 6 O LEU B 111 SHEET 7 AA1 7 ILE B 326 VAL B 328 -1 O ILE B 326 N VAL B 5 SHEET 1 AA2 7 SER B 189 ILE B 192 0 SHEET 2 AA2 7 ARG B 165 TRP B 169 1 N ALA B 166 O GLU B 191 SHEET 3 AA2 7 THR B 140 ILE B 144 1 N LEU B 141 O LEU B 167 SHEET 4 AA2 7 VAL B 204 THR B 207 1 O VAL B 204 N GLY B 142 SHEET 5 AA2 7 HIS B 229 ALA B 232 1 O ASN B 231 N ILE B 205 SHEET 6 AA2 7 SER B 297 ASP B 300 1 O PHE B 299 N ALA B 232 SHEET 7 AA2 7 PHE B 252 ALA B 255 1 N THR B 254 O VAL B 298 SHEET 1 AA3 7 GLY A 50 ARG A 54 0 SHEET 2 AA3 7 GLY A 60 GLU A 69 -1 O GLY A 60 N ARG A 54 SHEET 3 AA3 7 HIS A 73 TYR A 81 -1 O VAL A 79 N GLU A 63 SHEET 4 AA3 7 ILE A 94 ASP A 102 -1 O TYR A 101 N ILE A 74 SHEET 5 AA3 7 LEU A 108 ASP A 113 -1 O MET A 112 N VAL A 98 SHEET 6 AA3 7 THR A 3 LEU A 6 1 N LEU A 6 O LEU A 111 SHEET 7 AA3 7 ILE A 326 VAL A 328 -1 O ILE A 326 N VAL A 5 SHEET 1 AA4 7 SER A 189 ILE A 192 0 SHEET 2 AA4 7 ARG A 165 TRP A 169 1 N ALA A 166 O GLU A 191 SHEET 3 AA4 7 THR A 140 ILE A 144 1 N LEU A 141 O LEU A 167 SHEET 4 AA4 7 VAL A 204 THR A 207 1 O VAL A 204 N GLY A 142 SHEET 5 AA4 7 HIS A 229 ALA A 232 1 O ASN A 231 N ILE A 205 SHEET 6 AA4 7 SER A 297 ASP A 300 1 O PHE A 299 N ILE A 230 SHEET 7 AA4 7 PHE A 252 ALA A 255 1 N THR A 254 O VAL A 298 CISPEP 1 GLU B 56 PRO B 57 0 3.04 CISPEP 2 GLY B 216 PRO B 217 0 -3.33 CISPEP 3 GLN B 344 PRO B 345 0 1.55 CISPEP 4 GLU A 56 PRO A 57 0 0.85 CISPEP 5 GLY A 216 PRO A 217 0 5.43 SITE 1 AC1 36 LEU A 338 TYR B 81 THR B 93 ILE B 94 SITE 2 AC1 36 THR B 118 ARG B 121 THR B 122 ILE B 144 SITE 3 AC1 36 GLY B 147 ALA B 148 GLN B 149 ASP B 170 SITE 4 AC1 36 THR B 171 HIS B 175 ALA B 208 THR B 209 SITE 5 AC1 36 SER B 210 VAL B 211 VAL B 218 VAL B 233 SITE 6 AC1 36 GLY B 234 ALA B 235 ASP B 236 LYS B 240 SITE 7 AC1 36 SER B 301 THR B 302 GLY B 303 HOH B 525 SITE 8 AC1 36 HOH B 541 HOH B 567 HOH B 570 HOH B 589 SITE 9 AC1 36 HOH B 624 HOH B 632 HOH B 660 HOH B 667 SITE 1 AC2 8 GLY B 50 GLY B 51 GLU B 53 GLU B 63 SITE 2 AC2 8 ASP B 236 ARG B 263 GLU B 264 HOH B 532 SITE 1 AC3 36 TYR A 81 THR A 93 ILE A 94 THR A 118 SITE 2 AC3 36 ARG A 121 THR A 122 GLY A 147 ALA A 148 SITE 3 AC3 36 GLN A 149 ASP A 170 THR A 171 ASP A 172 SITE 4 AC3 36 HIS A 175 ALA A 208 THR A 209 SER A 210 SITE 5 AC3 36 VAL A 211 VAL A 218 VAL A 233 GLY A 234 SITE 6 AC3 36 ALA A 235 ASP A 236 LYS A 240 SER A 301 SITE 7 AC3 36 THR A 302 GLY A 303 HOH A 537 HOH A 538 SITE 8 AC3 36 HOH A 540 HOH A 547 HOH A 575 HOH A 611 SITE 9 AC3 36 HOH A 623 HOH A 652 HOH A 653 LEU B 338 SITE 1 AC4 9 GLY A 50 GLY A 51 GLU A 53 GLU A 63 SITE 2 AC4 9 ASP A 236 ARG A 263 GLU A 264 HOH A 548 SITE 3 AC4 9 HOH A 581 CRYST1 63.094 92.825 117.875 90.00 90.00 90.00 P 21 21 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 0.015849 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008484 0.00000