HEADER LYASE 28-SEP-16 5GZI 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: 25864; SOURCE 5 GENE: PIPA, SPRI_0308, SPRI_7045; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 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 5GZI 1 REMARK REVDAT 1 17-JAN-18 5GZI 0 JRNL AUTH H.YING,K.CHEN JRNL TITL CYCLODEAMINASE_PA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.17 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 35370 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1858 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) : 2.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2639 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.1920 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5237 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 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): 0.258 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.200 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.716 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5456 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5234 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7454 ; 1.652 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11999 ; 0.794 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 698 ; 7.347 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 228 ;36.155 ;22.588 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 819 ;14.068 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;20.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 865 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6179 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1210 ; 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): 2804 ; 2.971 ; 3.372 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2804 ; 2.971 ; 3.372 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3498 ; 4.160 ; 5.042 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3499 ; 4.159 ; 5.042 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2652 ; 3.274 ; 3.743 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2653 ; 3.274 ; 3.743 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3957 ; 4.823 ; 5.476 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6050 ; 7.568 ;27.526 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6050 ; 7.568 ;27.527 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5GZI 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_1300001719. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-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) : 1.5417 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37354 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.620 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 (%): 48.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 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: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.46300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.03000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.46300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.03000 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: 9230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 PRO B 347 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 351 REMARK 465 ALA A 352 REMARK 465 PRO A 353 REMARK 465 ALA A 354 REMARK 465 HIS A 355 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 NH1 ARG B 8 NE2 HIS A 0 1.66 REMARK 500 CD2 HIS A 0 OE2 GLU A 2 2.03 REMARK 500 O HOH B 604 O HOH B 615 2.06 REMARK 500 NH1 ARG A 43 O HOH A 501 2.09 REMARK 500 O GLY A 234 O HOH A 502 2.17 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 584 O HOH A 584 2859 1.50 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 B 54 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 54 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG B 182 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A -3 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 3.0 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 SER B 210 34.02 -85.70 REMARK 500 ALA B 235 123.31 173.47 REMARK 500 ASP B 236 -75.85 -150.50 REMARK 500 ASP B 323 74.74 13.84 REMARK 500 HIS B 333 74.49 -100.59 REMARK 500 PRO B 345 90.57 -32.23 REMARK 500 ASP A 72 -78.52 -108.95 REMARK 500 SER A 210 34.37 -92.31 REMARK 500 ALA A 235 128.86 179.15 REMARK 500 ASP A 236 -88.67 -160.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU B 343 GLN B 344 -126.84 REMARK 500 PRO B 345 LEU B 346 135.87 REMARK 500 REMARK 500 REMARK: NULL 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 YCP 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 YCP A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GZJ RELATED DB: PDB REMARK 900 RELATED ID: 5GZL RELATED DB: PDB REMARK 900 RELATED ID: 5GZM RELATED DB: PDB DBREF 5GZI B 1 355 UNP D9UBW0 D9UBW0_STRPR 1 355 DBREF 5GZI A 1 355 UNP D9UBW0 D9UBW0_STRPR 1 355 SEQADV 5GZI ARG B -3 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI GLY B -2 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI SER B -1 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI HIS B 0 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI ARG A -3 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI GLY A -2 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI SER A -1 UNP D9UBW0 EXPRESSION TAG SEQADV 5GZI 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 YCP B 402 9 HET NAD A 401 44 HET YCP A 402 9 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM YCP (2S)-PIPERIDINE-2-CARBOXYLIC ACID FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 YCP 2(C6 H11 N O2) FORMUL 7 HOH *239(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 ARG B 250 1 7 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 ALA B 290 5 5 HELIX 16 AB7 GLY B 291 THR B 295 5 5 HELIX 17 AB8 PHE B 304 ARG B 322 1 19 HELIX 18 AB9 GLY A 7 GLY A 19 1 13 HELIX 19 AC1 GLY A 19 ARG A 40 1 22 HELIX 20 AC2 ALA A 84 GLY A 90 1 7 HELIX 21 AC3 GLY A 114 ALA A 134 1 21 HELIX 22 AC4 GLY A 147 LEU A 161 1 15 HELIX 23 AC5 ASP A 172 SER A 178 1 7 HELIX 24 AC6 SER A 178 ALA A 184 1 7 HELIX 25 AC7 PHE A 185 GLY A 187 5 3 HELIX 26 AC8 GLU A 194 ALA A 202 1 9 HELIX 27 AC9 PRO A 244 ARG A 250 1 7 HELIX 28 AD1 HIS A 257 GLY A 265 1 9 HELIX 29 AD2 GLU A 266 LEU A 270 5 5 HELIX 30 AD3 SER A 271 LEU A 275 5 5 HELIX 31 AD4 GLN A 278 ASP A 285 1 8 HELIX 32 AD5 PRO A 286 ALA A 290 5 5 HELIX 33 AD6 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 TRP B 4 O THR B 109 SHEET 7 AA1 7 ILE B 326 VAL B 328 -1 O VAL B 328 N THR B 3 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 ARG B 165 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 ILE B 230 SHEET 7 AA2 7 PHE B 252 ALA B 255 1 N PHE B 252 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 THR A 75 N HIS A 67 SHEET 4 AA3 7 ILE A 94 ASP A 102 -1 O LEU A 95 N GLY A 80 SHEET 5 AA3 7 LEU A 108 ASP A 113 -1 O ALA A 110 N ARG A 100 SHEET 6 AA3 7 THR A 3 LEU A 6 1 N TRP A 4 O THR A 109 SHEET 7 AA3 7 ILE A 326 VAL A 328 -1 O VAL A 328 N THR A 3 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 SER A 189 SHEET 3 AA4 7 THR A 140 ILE A 144 1 N LEU A 141 O ARG A 165 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 ASP A 300 CISPEP 1 GLU B 56 PRO B 57 0 -0.83 CISPEP 2 GLY B 216 PRO B 217 0 1.50 CISPEP 3 GLU A 56 PRO A 57 0 -4.79 CISPEP 4 GLY A 216 PRO A 217 0 -5.66 SITE 1 AC1 32 LEU A 338 TYR B 81 THR B 93 ILE B 94 SITE 2 AC1 32 THR B 118 ARG B 121 THR B 122 GLY B 147 SITE 3 AC1 32 ALA B 148 GLN B 149 ASP B 170 THR B 171 SITE 4 AC1 32 ASP B 172 HIS B 175 THR B 209 SER B 210 SITE 5 AC1 32 VAL B 211 VAL B 218 VAL B 233 ALA B 235 SITE 6 AC1 32 ASP B 236 LYS B 240 SER B 301 THR B 302 SITE 7 AC1 32 GLY B 303 HOH B 512 HOH B 514 HOH B 523 SITE 8 AC1 32 HOH B 531 HOH B 533 HOH B 552 HOH B 571 SITE 1 AC2 9 ARG B 49 GLU B 63 MET B 65 LYS B 77 SITE 2 AC2 9 THR B 118 ARG B 121 ALA B 235 THR B 302 SITE 3 AC2 9 GLY B 303 SITE 1 AC3 31 TYR A 81 THR A 93 THR A 118 ARG A 121 SITE 2 AC3 31 THR A 122 GLY A 145 GLY A 147 ALA A 148 SITE 3 AC3 31 GLN A 149 ASP A 170 THR A 171 ASP A 172 SITE 4 AC3 31 HIS A 175 ALA A 208 THR A 209 SER A 210 SITE 5 AC3 31 VAL A 211 VAL A 218 VAL A 233 GLY A 234 SITE 6 AC3 31 ALA A 235 ASP A 236 LYS A 240 SER A 301 SITE 7 AC3 31 THR A 302 GLY A 303 YCP A 402 HOH A 527 SITE 8 AC3 31 HOH A 530 HOH A 542 HOH A 543 SITE 1 AC4 9 ARG A 49 GLU A 63 MET A 65 LYS A 77 SITE 2 AC4 9 ARG A 121 ALA A 235 THR A 302 GLY A 303 SITE 3 AC4 9 NAD A 401 CRYST1 136.926 74.060 95.718 90.00 132.72 90.00 C 1 2 1 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 0.007303 0.000000 0.006744 0.00000 SCALE2 0.000000 0.013503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014221 0.00000