HEADER HYDROLASE 15-MAY-17 5NZX TITLE CRYSTAL STRUCTURE OF DNA CROSS-LINK REPAIR PROTEIN 1A IN COMPLEX WITH TITLE 2 CEFTRIAXONE (ALTERNATIVE SITE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA CROSS-LINK REPAIR 1A PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SNM1 HOMOLOG A,HSNM1A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: DCLRE1A, KIAA0086, SNM1, SNM1A; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS EXONULCEASE, CEPHALOSPORIN, CROSS-LINK REPAIR, DCLRE1A, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.NEWMAN,H.AITKENHEAD,K.KUPINSKA,N.A.BURGESS-BROWN,R.TALON, AUTHOR 2 T.KROJER,F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS,C.BOUNTRA,O.GILEADI REVDAT 2 17-JAN-24 5NZX 1 REMARK REVDAT 1 14-JUN-17 5NZX 0 JRNL AUTH J.A.NEWMAN,H.AITKENHEAD,K.KUPINSKA,N.A.BURGESS-BROWN, JRNL AUTH 2 R.TALON,T.KROJER,F.VON DELFT,C.H.ARROWSMITH,A.EDWARDS, JRNL AUTH 3 C.BOUNTRA,O.GILEADI JRNL TITL CRYSTAL STRUCTURE OF DNA CROSS-LINK REPAIR PROTEIN 1A IN JRNL TITL 2 COMPLEX WITH CEFTRIAXONE (ALTERNATIVE SITE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 53912 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) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2840 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) : 1.47 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3635 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2640 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.28000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -0.81000 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): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.072 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.052 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.165 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2752 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2494 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3748 ; 1.346 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5796 ; 0.924 ; 2.993 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 334 ; 5.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;33.520 ;23.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 445 ;11.678 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;20.445 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 419 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3027 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 550 ; 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): 1342 ; 2.213 ; 2.605 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1341 ; 2.208 ; 2.604 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1674 ; 2.857 ; 3.919 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1675 ; 2.858 ; 3.920 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1410 ; 2.723 ; 2.903 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1408 ; 2.725 ; 2.902 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2073 ; 3.391 ; 4.245 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3099 ; 4.286 ;31.863 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3100 ; 4.285 ;31.865 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5246 ; 1.221 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 123 ;23.202 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5254 ;11.922 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 5NZX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1200004973. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61686 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 51.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.98500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 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: 5AHO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 % PEG 1000, 0.1 M MIB BUFFER PH REMARK 280 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 278K 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 25.72500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.76000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.27500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.76000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.72500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.27500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 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 LYS A 698 REMARK 465 HIS A 966 REMARK 465 SER A 967 REMARK 465 ASN A 968 REMARK 465 LYS A 969 REMARK 465 PHE A 970 REMARK 465 THR A 971 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 LYS A 699 CG CD CE NZ REMARK 470 GLU A 723 CG CD OE1 OE2 REMARK 470 GLN A 852 CG CD OE1 NE2 REMARK 470 ARG A 856 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 903 CG CD OE1 OE2 REMARK 470 LYS A 940 CG CD CE NZ REMARK 470 LYS A 947 CD CE NZ REMARK 470 ARG A 972 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 981 CE NZ 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 1361 O HOH A 1383 1.97 REMARK 500 O HOH A 1310 O HOH A 1383 2.18 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 1335 O HOH A 1391 3544 1.72 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 ALA A 739 117.47 -38.19 REMARK 500 HIS A 793 -112.87 -114.77 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 A1404 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A1405 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A1406 DISTANCE = 10.08 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 NI A1101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 732 NE2 REMARK 620 2 HIS A 734 ND1 87.8 REMARK 620 3 HIS A 793 NE2 95.2 92.3 REMARK 620 4 ASP A 815 OD2 88.0 171.0 96.0 REMARK 620 5 HOH A1310 O 92.2 90.7 172.1 81.5 REMARK 620 6 HOH A1361 O 175.3 92.9 89.4 90.6 83.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 1101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9F2 A 1102 DBREF 5NZX A 698 1040 UNP Q6PJP8 DCR1A_HUMAN 698 1040 SEQRES 1 A 343 LYS LYS THR CYS PRO PHE TYR LYS LYS ILE PRO GLY THR SEQRES 2 A 343 GLY PHE THR VAL ASP ALA PHE GLN TYR GLY VAL VAL GLU SEQRES 3 A 343 GLY CYS THR ALA TYR PHE LEU THR HIS PHE HIS SER ASP SEQRES 4 A 343 HIS TYR ALA GLY LEU SER LYS HIS PHE THR PHE PRO VAL SEQRES 5 A 343 TYR CYS SER GLU ILE THR GLY ASN LEU LEU LYS ASN LYS SEQRES 6 A 343 LEU HIS VAL GLN GLU GLN TYR ILE HIS PRO LEU PRO LEU SEQRES 7 A 343 ASP THR GLU CYS ILE VAL ASN GLY VAL LYS VAL VAL LEU SEQRES 8 A 343 LEU ASP ALA ASN HIS CYS PRO GLY ALA VAL MET ILE LEU SEQRES 9 A 343 PHE TYR LEU PRO ASN GLY THR VAL ILE LEU HIS THR GLY SEQRES 10 A 343 ASP PHE ARG ALA ASP PRO SER MET GLU ARG SER LEU LEU SEQRES 11 A 343 ALA ASP GLN LYS VAL HIS MET LEU TYR LEU ASP THR THR SEQRES 12 A 343 TYR CYS SER PRO GLU TYR THR PHE PRO SER GLN GLN GLU SEQRES 13 A 343 VAL ILE ARG PHE ALA ILE ASN THR ALA PHE GLU ALA VAL SEQRES 14 A 343 THR LEU ASN PRO HIS ALA LEU VAL VAL CYS GLY THR TYR SEQRES 15 A 343 SER ILE GLY LYS GLU LYS VAL PHE LEU ALA ILE ALA ASP SEQRES 16 A 343 VAL LEU GLY SER LYS VAL GLY MET SER GLN GLU LYS TYR SEQRES 17 A 343 LYS THR LEU GLN CYS LEU ASN ILE PRO GLU ILE ASN SER SEQRES 18 A 343 LEU ILE THR THR ASP MET CYS SER SER LEU VAL HIS LEU SEQRES 19 A 343 LEU PRO MET MET GLN ILE ASN PHE LYS GLY LEU GLN SER SEQRES 20 A 343 HIS LEU LYS LYS CYS GLY GLY LYS TYR ASN GLN ILE LEU SEQRES 21 A 343 ALA PHE ARG PRO THR GLY TRP THR HIS SER ASN LYS PHE SEQRES 22 A 343 THR ARG ILE ALA ASP VAL ILE PRO GLN THR LYS GLY ASN SEQRES 23 A 343 ILE SER ILE TYR GLY ILE PRO TYR SER GLU HIS SER SER SEQRES 24 A 343 TYR LEU GLU MET LYS ARG PHE VAL GLN TRP LEU LYS PRO SEQRES 25 A 343 GLN LYS ILE ILE PRO THR VAL ASN VAL GLY THR TRP LYS SEQRES 26 A 343 SER ARG SER THR MET GLU LYS TYR PHE ARG GLU TRP LYS SEQRES 27 A 343 LEU GLU ALA GLY TYR HET NI A1101 1 HET 9F2 A1102 36 HETNAM NI NICKEL (II) ION HETNAM 9F2 CEFTRIAXONE FORMUL 2 NI NI 2+ FORMUL 3 9F2 C18 H18 N8 O7 S3 FORMUL 4 HOH *206(H2 O) HELIX 1 AA1 PRO A 702 TYR A 704 5 3 HELIX 2 AA2 HIS A 734 ALA A 739 1 6 HELIX 3 AA3 SER A 752 LEU A 763 1 12 HELIX 4 AA4 GLN A 766 GLN A 768 5 3 HELIX 5 AA5 ASP A 819 GLN A 830 5 12 HELIX 6 AA6 SER A 850 ASN A 869 1 20 HELIX 7 AA7 LYS A 883 GLY A 895 1 13 HELIX 8 AA8 SER A 901 GLN A 909 1 9 HELIX 9 AA9 GLU A 915 SER A 918 5 4 HELIX 10 AB1 ASP A 923 SER A 927 5 5 HELIX 11 AB2 MET A 935 ILE A 937 5 3 HELIX 12 AB3 ASN A 938 LEU A 946 1 9 HELIX 13 AB4 LYS A 947 LYS A 952 5 6 HELIX 14 AB5 SER A 996 LYS A 1008 1 13 HELIX 15 AB6 THR A 1020 GLY A 1039 1 20 SHEET 1 AA1 5 LYS A 706 ILE A 707 0 SHEET 2 AA1 5 PHE A 712 VAL A 714 -1 O PHE A 712 N ILE A 707 SHEET 3 AA1 5 ALA A 727 PHE A 729 1 O PHE A 729 N THR A 713 SHEET 4 AA1 5 VAL A 749 CYS A 751 1 O TYR A 750 N TYR A 728 SHEET 5 AA1 5 ILE A 770 PRO A 772 1 O HIS A 771 N VAL A 749 SHEET 1 AA2 6 CYS A 779 VAL A 781 0 SHEET 2 AA2 6 VAL A 784 ASP A 790 -1 O VAL A 786 N CYS A 779 SHEET 3 AA2 6 VAL A 798 TYR A 803 -1 O LEU A 801 N VAL A 787 SHEET 4 AA2 6 VAL A 809 HIS A 812 -1 O ILE A 810 N PHE A 802 SHEET 5 AA2 6 MET A 834 LEU A 837 1 O TYR A 836 N LEU A 811 SHEET 6 AA2 6 LYS A1011 PRO A1014 1 O ILE A1013 N LEU A 835 SHEET 1 AA3 7 ILE A 920 THR A 921 0 SHEET 2 AA3 7 VAL A 898 GLY A 899 1 N VAL A 898 O THR A 921 SHEET 3 AA3 7 VAL A 929 PRO A 933 1 O VAL A 929 N GLY A 899 SHEET 4 AA3 7 ALA A 872 THR A 878 1 N VAL A 874 O HIS A 930 SHEET 5 AA3 7 GLN A 955 PRO A 961 1 O PHE A 959 N VAL A 875 SHEET 6 AA3 7 ILE A 984 ILE A 989 1 O TYR A 987 N ALA A 958 SHEET 7 AA3 7 GLN A 979 LYS A 981 -1 N GLN A 979 O ILE A 986 SSBOND 1 CYS A 925 CYS A 949 1555 1555 2.04 LINK NE2 HIS A 732 NI NI A1101 1555 1555 2.26 LINK ND1 HIS A 734 NI NI A1101 1555 1555 2.23 LINK NE2 HIS A 793 NI NI A1101 1555 1555 2.31 LINK OD2 ASP A 815 NI NI A1101 1555 1555 2.20 LINK NI NI A1101 O HOH A1310 1555 1555 2.10 LINK NI NI A1101 O HOH A1361 1555 1555 2.03 SITE 1 AC1 7 HIS A 732 HIS A 734 HIS A 793 ASP A 815 SITE 2 AC1 7 HOH A1310 HOH A1361 HOH A1383 SITE 1 AC2 20 ALA A 828 GLN A 830 LYS A 831 HIS A 833 SITE 2 AC2 20 ILE A 937 ASN A 938 PHE A 939 ARG A 960 SITE 3 AC2 20 THR A 962 LYS A 981 ILE A 986 GLY A 988 SITE 4 AC2 20 HOH A1220 HOH A1304 HOH A1313 HOH A1333 SITE 5 AC2 20 HOH A1382 HOH A1393 HOH A1405 HOH A1406 CRYST1 51.450 56.550 113.520 90.00 90.00 90.00 P 21 21 21 4 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 0.019436 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008809 0.00000