HEADER OXIDOREDUCTASE 26-SEP-16 5GZ6 TITLE STRUCTURE OF D-AMINO ACID DEHYDROGENASE IN COMPLEX WITH NADPH AND 2- TITLE 2 KETO-6-AMINOCAPRONIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESO-DIAMINOPIMELATE D-DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: MESO-DAP DEHYDROGENASE; COMPND 5 EC: 1.4.1.16; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UREIBACILLUS THERMOSPHAERICUS; SOURCE 3 ORGANISM_TAXID: 51173; SOURCE 4 GENE: DDH; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSSETA(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR H.SAKURABA,T.SETO,J.HAYASHI,H.AKITA,K.YONEDA,T.OHSHIMA REVDAT 4 08-NOV-23 5GZ6 1 REMARK REVDAT 3 06-DEC-17 5GZ6 1 JRNL REVDAT 2 31-MAY-17 5GZ6 1 JRNL REVDAT 1 12-APR-17 5GZ6 0 JRNL AUTH J.HAYASHI,T.SETO,H.AKITA,M.WATANABE,T.HOSHINO,K.YONEDA, JRNL AUTH 2 T.OHSHIMA,H.SAKURABA JRNL TITL STRUCTURE-BASED ENGINEERING OF AN ARTIFICIALLY GENERATED JRNL TITL 2 NADP+-DEPENDENT D-AMINO ACID DEHYDROGENASE JRNL REF APPL. ENVIRON. MICROBIOL. V. 83 2017 JRNL REFN ESSN 1098-5336 JRNL PMID 28363957 JRNL DOI 10.1128/AEM.00491-17 REMARK 2 REMARK 2 RESOLUTION. 1.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 71112 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3780 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) : 1.74 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.78 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5130 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.3440 REMARK 3 BIN FREE R VALUE SET COUNT : 291 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4920 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 397 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.80000 REMARK 3 B33 (A**2) : -0.74000 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): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.517 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 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): 5100 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4841 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6906 ; 2.357 ; 1.975 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11142 ; 1.215 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 629 ; 6.784 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 235 ;38.377 ;24.468 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 848 ;14.152 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;16.775 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 761 ; 0.156 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5775 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1154 ; 0.002 ; 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): 2537 ; 2.578 ; 2.525 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2536 ; 2.578 ; 2.525 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3158 ; 3.892 ; 3.758 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 48 REMARK 3 RESIDUE RANGE : A 49 A 149 REMARK 3 RESIDUE RANGE : A 150 A 256 REMARK 3 RESIDUE RANGE : A 257 A 326 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3186 95.1834 15.4279 REMARK 3 T TENSOR REMARK 3 T11: 0.0357 T22: 0.0243 REMARK 3 T33: 0.0424 T12: 0.0050 REMARK 3 T13: 0.0150 T23: 0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.3705 L22: 0.0749 REMARK 3 L33: 0.5955 L12: 0.1284 REMARK 3 L13: -0.0410 L23: -0.1434 REMARK 3 S TENSOR REMARK 3 S11: 0.0338 S12: -0.0790 S13: -0.0117 REMARK 3 S21: -0.0155 S22: -0.0335 S23: -0.0125 REMARK 3 S31: 0.0981 S32: 0.0256 S33: -0.0003 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 74 REMARK 3 RESIDUE RANGE : B 75 B 138 REMARK 3 RESIDUE RANGE : B 139 B 256 REMARK 3 RESIDUE RANGE : B 257 B 326 REMARK 3 ORIGIN FOR THE GROUP (A): 14.4280 96.1934 -16.2408 REMARK 3 T TENSOR REMARK 3 T11: 0.0953 T22: 0.0713 REMARK 3 T33: 0.0515 T12: -0.0315 REMARK 3 T13: 0.0382 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.5653 L22: 0.0169 REMARK 3 L33: 0.9555 L12: 0.0378 REMARK 3 L13: -0.6927 L23: -0.0161 REMARK 3 S TENSOR REMARK 3 S11: -0.1162 S12: 0.1852 S13: -0.0191 REMARK 3 S21: 0.0152 S22: 0.0254 S23: 0.0236 REMARK 3 S31: 0.1587 S32: -0.1971 S33: 0.0907 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 : WITH TLS ADDED REMARK 4 REMARK 4 5GZ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1300001704. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : SI REMARK 200 OPTICS : SILICON SINGLE CRYSTAL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74999 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.740 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 : 7.000 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.61700 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: 5GZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 6.5, VAPOR DIFFUSION, REMARK 280 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 27.41900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.39550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.38650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 69.39550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.41900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.38650 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: 6740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HIS A 156 REMARK 465 SER A 157 REMARK 465 SER A 259 REMARK 465 ASP A 260 REMARK 465 GLU A 261 REMARK 465 GLY A 262 REMARK 465 HIS A 263 REMARK 465 MET B 1 REMARK 465 HIS B 156 REMARK 465 SER B 157 REMARK 465 SER B 245 REMARK 465 GLY B 246 REMARK 465 SER B 259 REMARK 465 ASP B 260 REMARK 465 GLU B 261 REMARK 465 GLY B 262 REMARK 465 HIS B 263 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 A 124 109.06 -160.29 REMARK 500 PHE A 225 51.07 -94.20 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 NDP A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7C3 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 3002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GZ3 RELATED DB: PDB REMARK 900 RELATED ID: 5GZ1 RELATED DB: PDB DBREF 5GZ6 A 1 326 UNP G1UII1 DAPDH_URETH 1 326 DBREF 5GZ6 B 1 326 UNP G1UII1 DAPDH_URETH 1 326 SEQADV 5GZ6 ALA A 94 UNP G1UII1 ASP 94 ENGINEERED MUTATION SEQADV 5GZ6 LEU A 154 UNP G1UII1 GLN 154 ENGINEERED MUTATION SEQADV 5GZ6 GLY A 158 UNP G1UII1 ASP 158 ENGINEERED MUTATION SEQADV 5GZ6 ILE A 173 UNP G1UII1 THR 173 ENGINEERED MUTATION SEQADV 5GZ6 MET A 199 UNP G1UII1 ARG 199 ENGINEERED MUTATION SEQADV 5GZ6 PHE A 224 UNP G1UII1 TYR 224 ENGINEERED MUTATION SEQADV 5GZ6 ASN A 249 UNP G1UII1 HIS 249 ENGINEERED MUTATION SEQADV 5GZ6 ALA B 94 UNP G1UII1 ASP 94 ENGINEERED MUTATION SEQADV 5GZ6 LEU B 154 UNP G1UII1 GLN 154 ENGINEERED MUTATION SEQADV 5GZ6 GLY B 158 UNP G1UII1 ASP 158 ENGINEERED MUTATION SEQADV 5GZ6 ILE B 173 UNP G1UII1 THR 173 ENGINEERED MUTATION SEQADV 5GZ6 MET B 199 UNP G1UII1 ARG 199 ENGINEERED MUTATION SEQADV 5GZ6 PHE B 224 UNP G1UII1 TYR 224 ENGINEERED MUTATION SEQADV 5GZ6 ASN B 249 UNP G1UII1 HIS 249 ENGINEERED MUTATION SEQRES 1 A 326 MET SER LYS ILE ARG ILE GLY ILE VAL GLY TYR GLY ASN SEQRES 2 A 326 LEU GLY ARG GLY VAL GLU ALA ALA ILE GLN GLN ASN PRO SEQRES 3 A 326 ASP MET GLU LEU VAL ALA VAL PHE THR ARG ARG ASP PRO SEQRES 4 A 326 LYS THR VAL ALA VAL LYS SER ASN VAL LYS VAL LEU HIS SEQRES 5 A 326 VAL ASP ASP ALA GLN SER TYR LYS ASP GLU ILE ASP VAL SEQRES 6 A 326 MET ILE LEU CYS GLY GLY SER ALA THR ASP LEU PRO GLU SEQRES 7 A 326 GLN GLY PRO TYR PHE ALA GLN TYR PHE ASN THR ILE ASP SEQRES 8 A 326 SER PHE ALA THR HIS ALA ARG ILE PRO ASP TYR PHE ASP SEQRES 9 A 326 ALA VAL ASN ALA ALA ALA GLU GLN SER GLY LYS VAL ALA SEQRES 10 A 326 ILE ILE SER VAL GLY TRP ASP PRO GLY LEU PHE SER LEU SEQRES 11 A 326 ASN ARG LEU LEU GLY GLU VAL VAL LEU PRO VAL GLY ASN SEQRES 12 A 326 THR TYR THR PHE TRP GLY LYS GLY VAL SER LEU GLY HIS SEQRES 13 A 326 SER GLY ALA ILE ARG ARG ILE GLN GLY VAL LYS ASN ALA SEQRES 14 A 326 VAL GLN TYR ILE ILE PRO ILE ASP GLU ALA VAL ASN ARG SEQRES 15 A 326 VAL ARG SER GLY GLU ASN PRO GLU LEU SER THR ARG GLU SEQRES 16 A 326 LYS HIS ALA MET GLU CYS PHE VAL VAL LEU GLU GLU GLY SEQRES 17 A 326 ALA ASP PRO ALA LYS VAL GLU HIS GLU ILE LYS THR MET SEQRES 18 A 326 PRO ASN PHE PHE ASP GLU TYR ASP THR THR VAL HIS PHE SEQRES 19 A 326 ILE SER GLU GLU GLU LEU LYS GLN ASN HIS SER GLY MET SEQRES 20 A 326 PRO ASN GLY GLY PHE VAL ILE ARG SER GLY LYS SER ASP SEQRES 21 A 326 GLU GLY HIS LYS GLN ILE ILE GLU PHE SER LEU ASN LEU SEQRES 22 A 326 GLU SER ASN PRO MET PHE THR SER SER ALA LEU VAL ALA SEQRES 23 A 326 TYR ALA ARG ALA ALA TYR ARG LEU SER GLN ASN GLY ASP SEQRES 24 A 326 LYS GLY ALA LYS THR VAL PHE ASP ILE PRO PHE GLY LEU SEQRES 25 A 326 LEU SER PRO LYS SER PRO GLU ASP LEU ARG LYS GLU LEU SEQRES 26 A 326 LEU SEQRES 1 B 326 MET SER LYS ILE ARG ILE GLY ILE VAL GLY TYR GLY ASN SEQRES 2 B 326 LEU GLY ARG GLY VAL GLU ALA ALA ILE GLN GLN ASN PRO SEQRES 3 B 326 ASP MET GLU LEU VAL ALA VAL PHE THR ARG ARG ASP PRO SEQRES 4 B 326 LYS THR VAL ALA VAL LYS SER ASN VAL LYS VAL LEU HIS SEQRES 5 B 326 VAL ASP ASP ALA GLN SER TYR LYS ASP GLU ILE ASP VAL SEQRES 6 B 326 MET ILE LEU CYS GLY GLY SER ALA THR ASP LEU PRO GLU SEQRES 7 B 326 GLN GLY PRO TYR PHE ALA GLN TYR PHE ASN THR ILE ASP SEQRES 8 B 326 SER PHE ALA THR HIS ALA ARG ILE PRO ASP TYR PHE ASP SEQRES 9 B 326 ALA VAL ASN ALA ALA ALA GLU GLN SER GLY LYS VAL ALA SEQRES 10 B 326 ILE ILE SER VAL GLY TRP ASP PRO GLY LEU PHE SER LEU SEQRES 11 B 326 ASN ARG LEU LEU GLY GLU VAL VAL LEU PRO VAL GLY ASN SEQRES 12 B 326 THR TYR THR PHE TRP GLY LYS GLY VAL SER LEU GLY HIS SEQRES 13 B 326 SER GLY ALA ILE ARG ARG ILE GLN GLY VAL LYS ASN ALA SEQRES 14 B 326 VAL GLN TYR ILE ILE PRO ILE ASP GLU ALA VAL ASN ARG SEQRES 15 B 326 VAL ARG SER GLY GLU ASN PRO GLU LEU SER THR ARG GLU SEQRES 16 B 326 LYS HIS ALA MET GLU CYS PHE VAL VAL LEU GLU GLU GLY SEQRES 17 B 326 ALA ASP PRO ALA LYS VAL GLU HIS GLU ILE LYS THR MET SEQRES 18 B 326 PRO ASN PHE PHE ASP GLU TYR ASP THR THR VAL HIS PHE SEQRES 19 B 326 ILE SER GLU GLU GLU LEU LYS GLN ASN HIS SER GLY MET SEQRES 20 B 326 PRO ASN GLY GLY PHE VAL ILE ARG SER GLY LYS SER ASP SEQRES 21 B 326 GLU GLY HIS LYS GLN ILE ILE GLU PHE SER LEU ASN LEU SEQRES 22 B 326 GLU SER ASN PRO MET PHE THR SER SER ALA LEU VAL ALA SEQRES 23 B 326 TYR ALA ARG ALA ALA TYR ARG LEU SER GLN ASN GLY ASP SEQRES 24 B 326 LYS GLY ALA LYS THR VAL PHE ASP ILE PRO PHE GLY LEU SEQRES 25 B 326 LEU SER PRO LYS SER PRO GLU ASP LEU ARG LYS GLU LEU SEQRES 26 B 326 LEU HET NDP A1001 48 HET 7C3 A1002 10 HET SO4 A1003 5 HET ACT B3001 4 HET SO4 B3002 5 HETNAM NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM 2 NDP PHOSPHATE HETNAM 7C3 6-AZANYL-2-OXIDANYLIDENE-HEXANOIC ACID HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION FORMUL 3 NDP C21 H30 N7 O17 P3 FORMUL 4 7C3 C6 H11 N O3 FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 ACT C2 H3 O2 1- FORMUL 8 HOH *397(H2 O) HELIX 1 AA1 GLY A 12 GLN A 23 1 12 HELIX 2 AA2 ASP A 38 VAL A 42 5 5 HELIX 3 AA3 ASP A 54 LYS A 60 5 7 HELIX 4 AA4 THR A 74 ALA A 84 1 11 HELIX 5 AA5 THR A 95 ALA A 97 5 3 HELIX 6 AA6 ARG A 98 GLY A 114 1 17 HELIX 7 AA7 GLY A 126 LEU A 139 1 14 HELIX 8 AA8 ALA A 159 ILE A 163 5 5 HELIX 9 AA9 ILE A 176 GLY A 186 1 11 HELIX 10 AB1 SER A 192 LYS A 196 1 5 HELIX 11 AB2 ASP A 210 MET A 221 1 12 HELIX 12 AB3 SER A 236 HIS A 244 1 9 HELIX 13 AB4 MET A 278 ASN A 297 1 20 HELIX 14 AB5 THR A 304 ILE A 308 5 5 HELIX 15 AB6 PRO A 309 SER A 314 5 6 HELIX 16 AB7 SER A 317 LEU A 326 1 10 HELIX 17 AB8 GLY B 12 GLN B 23 1 12 HELIX 18 AB9 ASP B 38 VAL B 42 5 5 HELIX 19 AC1 ASP B 54 LYS B 60 5 7 HELIX 20 AC2 THR B 74 PHE B 87 1 14 HELIX 21 AC3 THR B 95 ALA B 97 5 3 HELIX 22 AC4 ARG B 98 GLY B 114 1 17 HELIX 23 AC5 GLY B 126 LEU B 139 1 14 HELIX 24 AC6 ALA B 159 ILE B 163 5 5 HELIX 25 AC7 ILE B 176 SER B 185 1 10 HELIX 26 AC8 SER B 192 LYS B 196 1 5 HELIX 27 AC9 ASP B 210 THR B 220 1 11 HELIX 28 AD1 SER B 236 HIS B 244 1 9 HELIX 29 AD2 MET B 278 ASN B 297 1 20 HELIX 30 AD3 THR B 304 ILE B 308 5 5 HELIX 31 AD4 PRO B 309 SER B 314 5 6 HELIX 32 AD5 SER B 317 LEU B 326 1 10 SHEET 1 AA1 7 LYS A 49 HIS A 52 0 SHEET 2 AA1 7 MET A 28 THR A 35 1 N VAL A 33 O LEU A 51 SHEET 3 AA1 7 ILE A 4 VAL A 9 1 N ILE A 6 O VAL A 31 SHEET 4 AA1 7 VAL A 65 LEU A 68 1 O ILE A 67 N GLY A 7 SHEET 5 AA1 7 ASN A 88 ASP A 91 1 O ILE A 90 N LEU A 68 SHEET 6 AA1 7 VAL A 116 ILE A 118 1 O ILE A 118 N THR A 89 SHEET 7 AA1 7 GLY A 301 LYS A 303 1 O LYS A 303 N ALA A 117 SHEET 1 AA212 THR A 230 PHE A 234 0 SHEET 2 AA212 HIS A 197 LEU A 205 1 N MET A 199 O THR A 231 SHEET 3 AA212 VAL A 166 PRO A 175 -1 N TYR A 172 O GLU A 200 SHEET 4 AA212 GLY A 142 GLY A 151 -1 N LYS A 150 O ILE A 173 SHEET 5 AA212 ASN A 249 GLY A 257 -1 O GLY A 250 N GLY A 149 SHEET 6 AA212 GLN A 265 GLU A 274 -1 O LEU A 273 N ASN A 249 SHEET 7 AA212 ILE B 266 GLU B 274 -1 O ASN B 272 N GLU A 268 SHEET 8 AA212 ASN B 249 GLY B 257 -1 N VAL B 253 O PHE B 269 SHEET 9 AA212 GLY B 142 VAL B 152 -1 N GLY B 149 O GLY B 250 SHEET 10 AA212 VAL B 166 PRO B 175 -1 O ILE B 173 N LYS B 150 SHEET 11 AA212 HIS B 197 LEU B 205 -1 O PHE B 202 N VAL B 170 SHEET 12 AA212 THR B 230 PHE B 234 1 O HIS B 233 N CYS B 201 SHEET 1 AA3 7 LYS B 49 HIS B 52 0 SHEET 2 AA3 7 MET B 28 THR B 35 1 N THR B 35 O LEU B 51 SHEET 3 AA3 7 ILE B 4 VAL B 9 1 N ILE B 8 O PHE B 34 SHEET 4 AA3 7 VAL B 65 LEU B 68 1 O ILE B 67 N GLY B 7 SHEET 5 AA3 7 THR B 89 ILE B 90 1 O ILE B 90 N LEU B 68 SHEET 6 AA3 7 VAL B 116 ILE B 118 1 O ILE B 118 N THR B 89 SHEET 7 AA3 7 GLY B 301 LYS B 303 1 O LYS B 303 N ALA B 117 CISPEP 1 ASP A 124 PRO A 125 0 -1.51 CISPEP 2 ASP B 124 PRO B 125 0 3.41 SITE 1 AC1 29 GLY A 10 TYR A 11 GLY A 12 ASN A 13 SITE 2 AC1 29 LEU A 14 THR A 35 ARG A 36 ARG A 37 SITE 3 AC1 29 CYS A 69 GLY A 70 GLY A 71 SER A 72 SITE 4 AC1 29 ASP A 75 SER A 92 ALA A 94 VAL A 121 SITE 5 AC1 29 GLY A 122 TRP A 123 ASP A 124 PRO A 125 SITE 6 AC1 29 THR A 280 7C3 A1002 HOH A1101 HOH A1128 SITE 7 AC1 29 HOH A1138 HOH A1253 ARG B 37 THR B 41 SITE 8 AC1 29 HOH B3101 SITE 1 AC2 5 ASP A 124 TRP A 148 LYS A 150 NDP A1001 SITE 2 AC2 5 HOH A1106 SITE 1 AC3 7 ASN A 249 LEU A 273 ASN A 276 PRO A 277 SITE 2 AC3 7 MET A 278 PHE A 279 HOH A1251 SITE 1 AC4 6 LEU A 130 ASN A 131 LEU B 127 ASN B 131 SITE 2 AC4 6 PHE B 310 HOH B3105 SITE 1 AC5 4 ARG A 37 ASP A 38 GLY B 12 ARG B 16 CRYST1 54.838 94.773 138.791 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 0.018236 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010552 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007205 0.00000