HEADER LYASE 13-MAR-14 4P53 TITLE VALA (2-EPI-5-EPI-VALIOLONE SYNTHASE) FROM STREPTOMYCES HYGROSCOPICUS TITLE 2 SUBSP. JINGGANGENSIS 5008 WITH NAD+ AND ZN2+ BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES HYGROSCOPICUS SUBSP. SOURCE 3 JINGGANGENSIS; SOURCE 4 ORGANISM_TAXID: 1133850; SOURCE 5 STRAIN: 5008; SOURCE 6 GENE: SHJG_0276; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE, SUGAR PHOSPHATE CYCLASE, PSEUDOGLYCOSIDE, SEDOHEPTULOSE 7- KEYWDS 2 PHOSPHATE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.KEAN,S.J.CODDING,P.A.KARPLUS REVDAT 5 27-SEP-23 4P53 1 REMARK REVDAT 4 11-DEC-19 4P53 1 REMARK LINK REVDAT 3 20-SEP-17 4P53 1 HEADER SOURCE JRNL REMARK REVDAT 2 01-OCT-14 4P53 1 JRNL REVDAT 1 30-JUL-14 4P53 0 JRNL AUTH K.M.KEAN,S.J.CODDING,S.ASAMIZU,T.MAHMUD,P.A.KARPLUS JRNL TITL STRUCTURE OF A SEDOHEPTULOSE 7-PHOSPHATE CYCLASE: VALA FROM JRNL TITL 2 STREPTOMYCES HYGROSCOPICUS. JRNL REF BIOCHEMISTRY V. 53 4250 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24832673 JRNL DOI 10.1021/BI5003508 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 20193 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1036 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 66.8788 - 4.0171 1.00 2922 144 0.1470 0.2242 REMARK 3 2 4.0171 - 3.1885 1.00 2778 143 0.1531 0.2409 REMARK 3 3 3.1885 - 2.7855 0.99 2720 170 0.1946 0.2730 REMARK 3 4 2.7855 - 2.5308 0.99 2754 124 0.2129 0.3131 REMARK 3 5 2.5308 - 2.3494 0.99 2717 133 0.2230 0.3011 REMARK 3 6 2.3494 - 2.2108 0.98 2650 157 0.2652 0.3226 REMARK 3 7 2.2108 - 2.1000 0.97 2616 165 0.2784 0.3441 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.010 2872 REMARK 3 ANGLE : 1.259 3906 REMARK 3 CHIRALITY : 0.051 463 REMARK 3 PLANARITY : 0.006 518 REMARK 3 DIHEDRAL : 13.991 1067 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 26:398 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.4467 45.4145 30.8642 REMARK 3 T TENSOR REMARK 3 T11: 0.2695 T22: 0.2369 REMARK 3 T33: 0.2553 T12: -0.0028 REMARK 3 T13: 0.0027 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.0811 L22: 2.0113 REMARK 3 L33: 2.6116 L12: -0.4575 REMARK 3 L13: 0.3295 L23: 0.0936 REMARK 3 S TENSOR REMARK 3 S11: 0.1251 S12: 0.1196 S13: -0.0933 REMARK 3 S21: -0.3375 S22: -0.0484 S23: 0.0165 REMARK 3 S31: -0.0104 S32: 0.3391 S33: -0.0653 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4P53 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000200701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 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 : DOUBLE-CRYSTAL, SI(111) LIQUID REMARK 200 N2 COOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 1.0.7 REMARK 200 DATA SCALING SOFTWARE : SCALA 2.0.6 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20232 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 66.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 26.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 19.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 STARTING MODEL: 3CLH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.6 M SUCCINIC ACID, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.04933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 33.02467 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 33.02467 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 66.04933 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: 8860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -103.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 99.07400 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CB PRO A 50 LIES ON A SPECIAL POSITION. 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 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 MET A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 GLN A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 LEU A 9 REMARK 465 SER A 10 REMARK 465 PRO A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 ARG A 14 REMARK 465 LEU A 15 REMARK 465 TYR A 16 REMARK 465 ASP A 17 REMARK 465 TYR A 18 REMARK 465 THR A 19 REMARK 465 THR A 20 REMARK 465 GLN A 21 REMARK 465 ASP A 22 REMARK 465 GLY A 23 REMARK 465 ALA A 24 REMARK 465 ALA A 25 REMARK 465 ASP A 46 REMARK 465 PRO A 47 REMARK 465 SER A 58 REMARK 465 GLY A 59 REMARK 465 THR A 60 REMARK 465 THR A 61 REMARK 465 PRO A 62 REMARK 465 GLY A 244 REMARK 465 GLU A 245 REMARK 465 GLY A 246 REMARK 465 GLY A 247 REMARK 465 THR A 248 REMARK 465 GLY A 249 REMARK 465 ARG A 399 REMARK 465 VAL A 400 REMARK 465 PRO A 401 REMARK 465 ARG A 402 REMARK 465 TRP A 403 REMARK 465 ARG A 404 REMARK 465 ALA A 405 REMARK 465 LEU A 406 REMARK 465 HIS A 407 REMARK 465 GLY A 408 REMARK 465 ALA A 409 REMARK 465 VAL A 410 REMARK 465 ASP A 411 REMARK 465 MET A 412 REMARK 465 GLY A 413 REMARK 465 VAL A 414 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 ARG A 43 CG CD NE CZ NH1 NH2 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 765 O HOH A 773 2.11 REMARK 500 O PRO A 50 OH TYR A 84 2.14 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 LEU A 45 CB ASN A 49 6765 0.92 REMARK 500 O LEU A 45 CG ASN A 49 6765 1.02 REMARK 500 C LEU A 45 ND2 ASN A 49 6765 1.23 REMARK 500 C LEU A 45 CG ASN A 49 6765 1.54 REMARK 500 O LEU A 45 ND2 ASN A 49 6765 1.82 REMARK 500 C LEU A 45 CB ASN A 49 6765 1.97 REMARK 500 O LEU A 45 OD1 ASN A 49 6765 1.99 REMARK 500 O LEU A 45 CA ASN A 49 6765 2.12 REMARK 500 CA LEU A 45 ND2 ASN A 49 6765 2.16 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 A 50 C - N - CA ANGL. DEV. = 12.6 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 ARG A 43 73.62 39.19 REMARK 500 ARG A 124 -9.25 -155.15 REMARK 500 ARG A 149 -2.39 77.80 REMARK 500 ALA A 150 128.93 173.11 REMARK 500 ASP A 165 -69.53 -148.76 REMARK 500 ARG A 177 -133.08 46.08 REMARK 500 ASN A 270 44.29 -149.70 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 ALA A 48 ASN A 49 -148.94 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 775 DISTANCE = 5.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 213 OE1 REMARK 620 2 HIS A 284 NE2 114.5 REMARK 620 3 HIS A 300 NE2 84.7 119.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 503 DBREF 4P53 A 1 414 UNP H2K887 H2K887_STRHJ 1 414 SEQADV 4P53 HIS A -5 UNP H2K887 EXPRESSION TAG SEQADV 4P53 HIS A -4 UNP H2K887 EXPRESSION TAG SEQADV 4P53 HIS A -3 UNP H2K887 EXPRESSION TAG SEQADV 4P53 HIS A -2 UNP H2K887 EXPRESSION TAG SEQADV 4P53 HIS A -1 UNP H2K887 EXPRESSION TAG SEQADV 4P53 HIS A 0 UNP H2K887 EXPRESSION TAG SEQRES 1 A 420 HIS HIS HIS HIS HIS HIS MET THR MET THR LYS GLN SER SEQRES 2 A 420 SER LEU SER PRO GLY SER ARG LEU TYR ASP TYR THR THR SEQRES 3 A 420 GLN ASP GLY ALA ALA TRP ARG VAL SER ALA LEU LYS GLU SEQRES 4 A 420 VAL SER TYR ASP VAL VAL VAL GLN PRO ARG LEU LEU ASP SEQRES 5 A 420 PRO ALA ASN PRO ALA LEU ALA ASP ALA LEU SER SER GLY SEQRES 6 A 420 THR THR PRO ALA ARG ARG LEU ILE VAL ILE ASP ALA THR SEQRES 7 A 420 VAL ARG SER LEU TYR GLY GLU GLN LEU ALA ALA TYR LEU SEQRES 8 A 420 ALA GLY HIS ASP VAL GLU PHE HIS LEU CYS VAL ILE ASP SEQRES 9 A 420 ALA HIS GLU SER ALA LYS VAL MET GLU THR VAL PHE GLU SEQRES 10 A 420 VAL VAL ASP ALA MET ASP ALA PHE GLY VAL PRO ARG ARG SEQRES 11 A 420 HIS ALA PRO VAL LEU ALA MET GLY GLY GLY VAL LEU THR SEQRES 12 A 420 ASP ILE VAL GLY LEU ALA ALA SER LEU TYR ARG ARG ALA SEQRES 13 A 420 THR PRO TYR VAL ARG ILE PRO THR THR LEU ILE GLY MET SEQRES 14 A 420 ILE ASP ALA GLY ILE GLY ALA LYS THR GLY VAL ASN PHE SEQRES 15 A 420 ARG GLU HIS LYS ASN ARG LEU GLY THR TYR HIS PRO SER SEQRES 16 A 420 SER LEU THR LEU ILE ASP PRO GLY PHE LEU ALA THR LEU SEQRES 17 A 420 ASP ALA ARG HIS LEU ARG ASN GLY LEU ALA GLU ILE LEU SEQRES 18 A 420 LYS VAL ALA LEU VAL LYS ASP ALA GLU LEU PHE ASP LEU SEQRES 19 A 420 LEU GLU GLY HIS GLY ALA SER LEU VAL GLU GLN ARG MET SEQRES 20 A 420 GLN PRO GLY GLU GLY GLY THR GLY GLY ALA ALA LEU THR SEQRES 21 A 420 VAL LEU ARG ARG ALA VAL GLN GLY MET LEU GLU GLU LEU SEQRES 22 A 420 GLN PRO ASN LEU TRP GLU HIS GLN LEU ARG ARG LEU VAL SEQRES 23 A 420 ASP PHE GLY HIS SER PHE SER PRO SER VAL GLU MET ALA SEQRES 24 A 420 ALA LEU PRO GLU LEU LEU HIS GLY GLU ALA VAL CYS ILE SEQRES 25 A 420 ASP MET ALA LEU SER SER VAL LEU ALA HIS HIS ARG GLY SEQRES 26 A 420 LEU LEU THR GLU ALA GLU LEU GLY ARG VAL LEU ASP VAL SEQRES 27 A 420 MET ARG LEU LEU HIS LEU PRO VAL LEU HIS PRO VAL CYS SEQRES 28 A 420 THR PRO ASP LEU MET ARG ALA ALA LEU ALA ASP THR VAL SEQRES 29 A 420 LYS HIS ARG ASP GLY TRP GLN HIS MET PRO LEU PRO ARG SEQRES 30 A 420 GLY ILE GLY ASP ALA VAL PHE VAL ASN ASP VAL THR GLN SEQRES 31 A 420 ARG GLU ILE GLU ALA ALA LEU LEU THR LEU ALA GLU ARG SEQRES 32 A 420 ASP ARG VAL PRO ARG TRP ARG ALA LEU HIS GLY ALA VAL SEQRES 33 A 420 ASP MET GLY VAL HET ZN A 501 1 HET NAI A 502 44 HET PEG A 503 7 HETNAM ZN ZINC ION HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN NAI NADH FORMUL 2 ZN ZN 2+ FORMUL 3 NAI C21 H29 N7 O14 P2 FORMUL 4 PEG C4 H10 O3 FORMUL 5 HOH *188(H2 O) HELIX 1 AA1 LEU A 52 SER A 57 1 6 HELIX 2 AA2 ALA A 71 HIS A 88 1 18 HELIX 3 AA3 HIS A 100 LYS A 104 5 5 HELIX 4 AA4 VAL A 105 GLY A 120 1 16 HELIX 5 AA5 GLY A 133 TYR A 147 1 15 HELIX 6 AA6 ARG A 148 ALA A 150 5 3 HELIX 7 AA7 THR A 159 ASP A 165 1 7 HELIX 8 AA8 ASP A 195 LEU A 202 5 8 HELIX 9 AA9 ASP A 203 ASP A 222 1 20 HELIX 10 AB1 ASP A 222 GLN A 239 1 18 HELIX 11 AB2 ALA A 251 GLN A 268 1 18 HELIX 12 AB3 PRO A 269 LEU A 271 5 3 HELIX 13 AB4 ARG A 278 PHE A 282 5 5 HELIX 14 AB5 PHE A 286 LEU A 295 1 10 HELIX 15 AB6 LEU A 299 ARG A 318 1 20 HELIX 16 AB7 THR A 322 LEU A 336 1 15 HELIX 17 AB8 THR A 346 ARG A 361 1 16 HELIX 18 AB9 THR A 383 ASP A 398 1 16 SHEET 1 AA1 6 ASP A 37 VAL A 40 0 SHEET 2 AA1 6 LEU A 191 ILE A 194 1 O THR A 192 N VAL A 39 SHEET 3 AA1 6 TYR A 153 PRO A 157 1 N ARG A 155 O LEU A 191 SHEET 4 AA1 6 VAL A 128 GLY A 132 1 N ALA A 130 O VAL A 154 SHEET 5 AA1 6 ARG A 64 ASP A 70 1 N VAL A 68 O LEU A 129 SHEET 6 AA1 6 GLU A 91 ILE A 97 1 O CYS A 95 N ILE A 67 SHEET 1 AA2 2 LYS A 171 PHE A 176 0 SHEET 2 AA2 2 HIS A 179 TYR A 186 -1 O LEU A 183 N VAL A 174 SHEET 1 AA3 2 MET A 367 PRO A 370 0 SHEET 2 AA3 2 ALA A 376 VAL A 379 -1 O VAL A 377 N LEU A 369 LINK OE1 GLU A 213 ZN ZN A 501 1555 1555 2.08 LINK NE2 HIS A 284 ZN ZN A 501 1555 1555 2.09 LINK NE2 HIS A 300 ZN ZN A 501 1555 1555 1.97 CISPEP 1 LEU A 295 PRO A 296 0 6.69 SITE 1 AC1 4 GLU A 213 HIS A 284 HIS A 300 HOH A 707 SITE 1 AC2 28 ASP A 70 THR A 72 VAL A 73 LEU A 76 SITE 2 AC2 28 GLU A 101 LYS A 104 GLY A 133 GLY A 134 SITE 3 AC2 28 VAL A 135 ASP A 138 THR A 158 THR A 159 SITE 4 AC2 28 ILE A 161 ASP A 165 ALA A 166 LYS A 171 SITE 5 AC2 28 LYS A 180 ASN A 181 PHE A 198 THR A 201 SITE 6 AC2 28 HIS A 206 ASN A 209 HOH A 663 HOH A 667 SITE 7 AC2 28 HOH A 714 HOH A 724 HOH A 728 HOH A 770 SITE 1 AC3 6 SER A 29 GLN A 261 GLU A 265 GLN A 268 SITE 2 AC3 6 HOH A 605 HOH A 648 CRYST1 77.186 77.186 99.074 90.00 90.00 120.00 P 32 2 1 6 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 0.012956 0.007480 0.000000 0.00000 SCALE2 0.000000 0.014960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010094 0.00000